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Chatziefthimiou AD, Metcalf JS, Glover WB, Powell JT, Banack SA, Cox PA, Ladjimi M, Sultan AA, Chemaitelly H, Richer RA. Cyanotoxin accumulation and growth patterns of biocrust communities under variable environmental conditions. Toxicon X 2024; 23:100199. [PMID: 38974839 PMCID: PMC11225906 DOI: 10.1016/j.toxcx.2024.100199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024] Open
Abstract
Biocrusts dominate the soil surface in deserts and are composed of diverse microbial communities that provide important ecosystem services. Cyanobacteria in biocrusts produce many secondary metabolites, including the neurotoxins BMAA, AEG, DAB, anatoxin-a(S) (guanitoxin), and the microcystin hepatotoxins, all known or suspected to cause disease or illness in humans and other animals. We examined cyanobacterial growth and prevalence of these toxins in biocrusts at millimeter-scales, under a desert-relevant illumination gradient. In contrast to previous work, we showed that hydration had an overall positive effect on growth and toxin accumulation, that nitrogen was not correlated with growth or toxin production, and that phosphorus enrichment negatively affected AEG and BMAA concentrations. Excess illumination positively correlated with AEG, and negatively correlated with all other toxins and growth. Basic pH negatively affected only the accumulation of BMAA. Anatoxin-a(S) (guanitoxin) was not correlated with any tested variables, while microcystins were not detected in any of the samples. Concerning toxin pools, AEG and BMAA were good predictors of the presence of one another. In a newly conceptualized scheme, we integrate aspects of biocrust growth and toxin pool accumulations with arid-relevant desertification drivers.
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Affiliation(s)
| | - James S. Metcalf
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
- Bowling Green State University, Bowling Green, OH, USA
| | | | - James T. Powell
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
| | - Sandra A. Banack
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
| | - Paul A. Cox
- Brain Chemistry Labs, Institute for Ethnomedicine, Jackson, WY, USA
| | - Moncef Ladjimi
- Weill Cornell Medicine – Qatar, Education City, Doha, Qatar
| | - Ali A. Sultan
- Weill Cornell Medicine – Qatar, Education City, Doha, Qatar
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2
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Wang L, Li J, Zhang S, Huang Y, Ouyang Z, Mai Z. Biological soil crust elicits microbial community and extracellular polymeric substances restructuring to reduce the soil erosion on tropical island, South China Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106449. [PMID: 38492504 DOI: 10.1016/j.marenvres.2024.106449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Soil erosion stands as the preeminent environmental concern globally, attaining heightened significance, particularly within islands where land resources prove notably scarce. Biological soil crusts, referred to as biocrusts, assume a pivotal ecological role in soil conservation. Notably, they augment the horizontal stability of the substrate through the exudation of microbial extracellular polymeric substances (EPS), thereby shielding the soil against shear stress, exemplified in the form of water erosion. While extant research has delved into the anti-erosion mechanisms of biocrusts in arid landscapes, a conspicuous lacuna persists in the exploration of coral island environments. In this study, we collected and assessed 30 samples encompassing dark biocrusts, light biocrusts, and bare soil to scrutinize the potential anti-erosion efficacy of tropical coral island biocrusts within the South China Sea. Employing a cohesive strength meter, we quantified soil shear stress across various stages of biocrust development, revealing a discernible enhancement in soil erosion resistance during the formation of biocrusts. Relative to the exposed bare soil, the soil shear stress exhibited an escalation from 0.33 N m-2 to 0.61 N m-2 and 1.31 N m-2 in the light biocrusts and dark biocrusts, respectively. Mechanistically, we assayed microbial EPS contents, exposing a positive correlation between EPS and soil anti-erodibility, encompassing extracellular protein and polysaccharide. Concurrently, bacterial abundance displayed a significant augmentation commensurate with biocrust formation and development. In pursuit of elucidating the origin of EPS, high-throughput amplicon sequencing was executed to identify microorganisms contributing to biocrust development. Correlation analysis discerned Cyanobacteria, Chloroflexi, Deinococcota, and Patescibacteria as potential microbials fostering EPS production and fortifying erosion resistance. Collectively, our study presents the first evidence that biocrust from tropical coral reef island in the South China Sea promotes resistance to soil erosion, pinpointing key EPS-producing microbials against soil erosion. The findings would provide insights for island environment restoration.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong, PR China
| | - Yadong Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Zhiyuan Ouyang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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Wang L, Huang Y, Yang Q, Mai Z, Xie F, Lyu L, Zhang S, Li J. Biocrust reduces the soil erodibility of coral calcareous sand by regulating microbial community and extracellular polymeric substances on tropical coral island, South China Sea. Front Microbiol 2023; 14:1283073. [PMID: 38152373 PMCID: PMC10751374 DOI: 10.3389/fmicb.2023.1283073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
Tropical coral islands assume a pivotal role in the conservation of oceanic ecosystem biodiversity. However, their distinctive environmental attributes and limited vegetation render them highly susceptible to soil erosion. The biological soil crust (biocrust), owing to its significant ecological role in soil stabilization and erosion prevention, is deemed an effective means of mitigating soil erosion on coral island. However, existing research on the mechanisms through which biocrusts resist soil erosion has predominantly concentrated on arid and semi-arid regions. Consequently, this study will specifically delve into elucidating the erosion-resistant mechanisms of biocrusts in tropical coral island environments, South China Sea. Specifically, we collected 16 samples of biocrusts and bare soil from Meiji Island. High-throughput amplicon sequencing was executed to analyze the microbial community, including bacteria, fungi, and archaea. Additionally, quantitative PCR was utilized to assess the abundance of the bacterial 16S rRNA, fungal ITS, archaeal 16S rRNA, and cyanobacterial 16S rRNA genes within these samples. Physicochemical measurements and assessments of extracellular polymeric substances (EPSs) were conducted to characterize the soil properties. The study reported a significantly decreased soil erodibility factor after biocrust formation. Compared to bare soil, soil erodibility factor decreased from 0.280 to 0.190 t h MJ-1 mm-1 in the biocrusts. Mechanistically, we measured the microbial EPS contents and revealed a negative correlation between EPS and soil erodibility factor. Consistent with increased EPS, the abundance of bacteria, fungi, archaea, and cyanobacteria were also detected significantly increased with biocrust formation. Correlation analysis detected Cyanobacteria, Chloroflexi, Deinococcota, and Crenarchaeota as potential microbials promoting EPSs and reducing soil erosion. Together, our study presents the evidence that biocrust from tropical coral island in the South China Sea promotes resistance to soil erosion, pinpointing key EPSs-producing microbials against soil erosion. The findings would provide insights for island soil restoration.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yu Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Feiyang Xie
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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Stebegg R, Schmetterer G, Rompel A. Heterotrophy among Cyanobacteria. ACS OMEGA 2023; 8:33098-33114. [PMID: 37744813 PMCID: PMC10515406 DOI: 10.1021/acsomega.3c02205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/10/2023] [Indexed: 09/26/2023]
Abstract
Cyanobacteria have been studied in recent decades to investigate the principle mechanisms of plant-type oxygenic photosynthesis, as they are the inventors of this process, and their cultivation and research is much easier compared to land plants. Nevertheless, many cyanobacterial strains possess the capacity for at least some forms of heterotrophic growth. This review demonstrates that cyanobacteria are much more than simple photoautotrophs, and their flexibility toward different environmental conditions has been underestimated in the past. It summarizes the strains capable of heterotrophy known by date structured by their phylogeny and lists the possible substrates for heterotrophy for each of them in a table in the Supporting Information. The conditions are discussed in detail that cause heterotrophic growth for each strain in order to allow for reproduction of the results. The review explains the importance of this knowledge for the use of new methods of cyanobacterial cultivation, which may be advantageous under certain conditions. It seeks to stimulate other researchers to identify new strains capable of heterotrophy that have not been known so far.
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Affiliation(s)
- Ronald Stebegg
- Universität Wien, Fakultät für Chemie, Institut für
Biophysikalische Chemie, 1090 Wien, Austria
| | - Georg Schmetterer
- Universität Wien, Fakultät für Chemie, Institut für
Biophysikalische Chemie, 1090 Wien, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für
Biophysikalische Chemie, 1090 Wien, Austria
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6
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Abstract
Biological soil crusts are thin, inconspicuous communities along the soil atmosphere ecotone that, until recently, were unrecognized by ecologists and even more so by microbiologists. In its broadest meaning, the term biological soil crust (or biocrust) encompasses a variety of communities that develop on soil surfaces and are powered by photosynthetic primary producers other than higher plants: cyanobacteria, microalgae, and cryptogams like lichens and mosses. Arid land biocrusts are the most studied, but biocrusts also exist in other settings where plant development is constrained. The minimal requirement is that light impinge directly on the soil; this is impeded by the accumulation of plant litter where plants abound. Since scientists started paying attention, much has been learned about their microbial communities, their composition, ecological extent, and biogeochemical roles, about how they alter the physical behavior of soils, and even how they inform an understanding of early life on land. This has opened new avenues for ecological restoration and agriculture.
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Affiliation(s)
- Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, Arizona, USA;
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7
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Hansen FA, James DK, Anderson JP, Meredith CS, Dominguez AJ, Pombubpa N, Stajich JE, Romero-Olivares AL, Salley SW, Pietrasiak N. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert. Front Microbiol 2023; 14:1135800. [PMID: 37350785 PMCID: PMC10282155 DOI: 10.3389/fmicb.2023.1135800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. Methods This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity. Results Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Discussion Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.
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Affiliation(s)
- Frederick A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Darren K. James
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | - John P. Anderson
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | | | - Andrew J. Dominguez
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
| | - Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | | | - Shawn W. Salley
- U.S. Department of Agriculture-Natural Resources Conservation Service, Jornada Experimental Range, Las Cruces, NM, United States
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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Wang J, Xiao J, Zhang Z, Yang L, Liu Z, Cheng Y, Wu L. Changes of bacterial community structure,monosaccharide composition and CO 2 exchange along the successional stages of biological soil crusts. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023:10.1007/s10653-023-01572-1. [PMID: 37147551 DOI: 10.1007/s10653-023-01572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/09/2023] [Indexed: 05/07/2023]
Abstract
Biological soil crusts (BSCs) are a dominant ecological landscape of drylands, which have a significant impact on global biogeochemical flux. However, it is unclear how bacterial community and physiological characteristics vary along the BSCs successional stages. In this study, bacterial community composition, physiological characteristics, and monosaccharide composition of extracellular polysaccharides (EPSs) were compared among different successional stages. Our findings demonstrated that besides the dominant bacterial species, the bacterial communities also showed considerable differences between these two stages. Cyanobacteria were keystone taxa in the early stage, while heterotrophic bacteria (Proteobacteria, Actinobacteria and Acidobacteria) were keystone taxa in the later stages. According to the results of CO2 exchange, cyanobacterial crusts accumulated net carbon faster than moss crusts, while moss crusts had a significantly higher respiration rate. The monosaccharide analysis indicated that the EPSs components also varied depending on BSCs' successional stages. Specifically, the contents of rhamnose and arabinose were higher in the cyanobacterial crusts than other types of crusts, while the contents of fucose, xylose, mannose and glucose were the highest in cyanobacterial-lichen crusts, and galactose content was highest in the moss crusts. Altogether, our results stress the heterogeneous variation of BSCs along with succession, and this work offered a fresh viewpoint for a deeper comprehension of the interactions between the monosaccharide components of EPS and the networks of bacterial communities in BSCs.
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Affiliation(s)
- Jiping Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China
| | - Jingshang Xiao
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China
| | - Zulin Zhang
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China
- The James Hutton Institute, Craigie Buckler, Aberdeen, ABI5 8QH, UK
| | - Lie Yang
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China
| | - Zhe Liu
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China
| | - Yongtao Cheng
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China
| | - Li Wu
- School of Resources and Environmental Engineering, Wuhan University of Technology, 430072, Wuhan, China.
- State Environmental Protection, Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 130117, Changchun, China.
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Pérez-Uz B, Galfione VC, Ochoa-Hueso R, Martín-Cereceda M. Protist Diversity Responses to Experimental N Deposition in Biological Crusts of a Semiarid Mediterranean Ecosystem. Protist 2023; 174:125929. [PMID: 36455480 DOI: 10.1016/j.protis.2022.125929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/17/2022]
Abstract
Biological soil crusts (BSC) are associations of different macro and microorganisms and aggregated soil particles located on the surface of soils in many different habitats. BSC harbour a diverse and complex community of ciliates and testate amoebae. These phagotrophic protists play an important role in C and N recycling in soil ecosystems but have not been frequently studied in BSC. In this context, the effects of three increasing N inputs on ciliates and testate amoebae in crusts from a semi-arid Mediterranean ecosystem were evaluated. A field experiment with artificial N-deposition was designed to mimic the effects caused by anthropogenic N depositions. The results have shown that the protist populations of these semi-arid Mediterranean environments have lower species richness than other soil environments. The increase in N produces a net loss of diversity in the populations studied and shifts in the community structure. It has also been shown that some ciliates and testate amoebae, due to their population responses to increased N concentrations, could potentially be used as bio-indicators of N contamination in these BSCs.
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Affiliation(s)
- Blanca Pérez-Uz
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
| | - Virginia C Galfione
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Raul Ochoa-Hueso
- Instituto de Investigación Vitivinicola y Agroalimentaria, Universidad de Cádiz, Puerto Real, Spain
| | - Mercedes Martín-Cereceda
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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10
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Peng Z, Wei S, Hu Y, Qi B, Yuan C, Wang Q, Li Y. Assessment of Fungal Diversity in Minqin County, a Typical Arid Region in Northwestern China. Curr Microbiol 2023; 80:62. [PMID: 36593374 DOI: 10.1007/s00284-022-03167-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023]
Abstract
Minqin County is located in the Shiyang River Basin. As a typical arid area, it is eroded by the Badain Jaran and Tengger Desert all year round, and knowledge of the fungal diversity in this area is limited. Therefore, fungal community structure and distribution in the soil of the artificial forest, desert transition zone, farmland, and desert were investigated using amplicon sequencing of the fungal ITS gene. Ten fungal phyla and 23 classes were identified, including 1131 fungi OTUs, Sordariomycetes, Dothideomycetes, Pezizomycetes, and Agaricomycetes were the most abundant classes. Although most OTUs are shared among habitats, fungal community composition among samples was highly variable, which may influence the design of restoration practices in this area.
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Affiliation(s)
- Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China
| | - Shuwei Wei
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yaping Hu
- Nanjing Institute of Environmental Science, Nanjing, China
| | - Bao Qi
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Chaofeng Yuan
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Qi Wang
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.
| | - Yu Li
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
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11
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Nelson C, Giraldo-Silva A, Warsop Thomas F, Garcia-Pichel F. Spatial self-segregation of pioneer cyanobacterial species drives microbiome organization in biocrusts. ISME COMMUNICATIONS 2022; 2:114. [PMID: 37938289 PMCID: PMC9723579 DOI: 10.1038/s43705-022-00199-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2023]
Abstract
Microbial communities are typically characterized by some degree of self-organization. In biological soil crust (biocrust) communities, vertical organization of resident populations at the mm scale is driven by organismal adaptations to physicochemical microniches. However, the extent of horizontal organization and its driving processes are unknown. Using a combination of observational and genetic mapping, we provide evidence for a highly defined, horizontal self-organization (patchiness) at the mm to cm scale in a successionally early biocrust community dominated by the pioneer cyanobacteria, Microcoleus vaginatus (Microcoleaceae) and Parifilum sp. (Coleofasciculaceae). Experiments with representative isolates of each species demonstrate that the phenomenon is driven by active spatial segregation based on cross-species sensing through the exometabolome acted upon with motility responses. Further, we show that both species share the ability to enrich for specialized cyanospheres of heterotrophic bacteria at smaller scales, and that these cyanospheres are characterized by compositional host-specificity, thus expanding the reach of spatial patchiness beyond primary producers. Our results highlight the importance of specific microbial interactions in the emergence of microbiome compositional architecture and the enhancement of microbial diversity.
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Affiliation(s)
- Corey Nelson
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Ana Giraldo-Silva
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Finlay Warsop Thomas
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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12
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García-Carmona M, Lepinay C, García-Orenes F, Baldrian P, Arcenegui V, Cajthaml T, Mataix-Solera J. Moss biocrust accelerates the recovery and resilience of soil microbial communities in fire-affected semi-arid Mediterranean soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157467. [PMID: 35868386 DOI: 10.1016/j.scitotenv.2022.157467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
After wildfires in Mediterranean ecosystems, ruderal mosses are pioneer species, stabilizing the soil surface previous to the establishment of vascular vegetation. However, little is known about the implication of pioneer moss biocrusts for the recovery and resilience of soils in early post-fire stages in semi-arid areas. Therefore, we studied the effects of the burgeoning biocrust on soil physicochemical and biochemical properties and the diversity and composition of microbial communities after a moderate-to-high wildfire severity. Seven months after the wildfire, the biocrust softened the strong impact of the fire in soils, affecting the diversity and composition of bacteria and fungi community compared to the uncrusted soils exposed to unfavourable environmental stress. Soil moisture, phosphorous, and enzyme activities representing the altered biogeochemical cycles after the fire, were the main explanatory variables for biocrust microbial community composition under the semi-arid conditions. High bacterial diversity was found in soils under mosses, while long-lasting legacies are expected in the fungal community, which showed greater sensitivity to the fire. The composition of bacterial and fungal communities at several taxonomical levels was profoundly altered by the presence of the moss biocrust, showing a rapid successional transition toward the unburned soil community. Pioneer moss biocrust play an important role improving the resilience of soil microbial communities. In the context of increasing fire intensity, studying the moss biocrust effects on the recovery of soils microbiome is essential to understanding the resistance and resilience of Mediterranean forests to wildfires.
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Affiliation(s)
- Minerva García-Carmona
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain.
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Fuensanta García-Orenes
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Victoria Arcenegui
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Jorge Mataix-Solera
- GEA-Environmental Soil Science Group, Department of Agrochemistry and Environment, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche, Spain
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13
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Chilton AM, Nguyen STT, Nelson TM, Pearson LA, Neilan BA. Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts). Environ Microbiol 2022; 24:5467-5482. [PMID: 35769014 PMCID: PMC9796556 DOI: 10.1111/1462-2920.16098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/07/2022] [Indexed: 01/01/2023]
Abstract
The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or 'biocrusts'. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more diverse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M. paludosus dominating in the north and M. vaginatus dominating in the south. The geographical shifts in bacterial composition and diversity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for sampling strategies to maximize access to bacterial genetic diversity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi-arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.
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Affiliation(s)
- Angela M. Chilton
- School of Biotechnology and Biomolecular SciencesUniversity of New South WalesNew South WalesAustralia
| | - Suong T. T. Nguyen
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Tiffanie M. Nelson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Leanne A. Pearson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Brett A. Neilan
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
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14
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Kratz AM, Maier S, Weber J, Kim M, Mele G, Gargiulo L, Leifke AL, Prass M, Abed RMM, Cheng Y, Su H, Pöschl U, Weber B. Reactive Nitrogen Hotspots Related to Microscale Heterogeneity in Biological Soil Crusts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11865-11877. [PMID: 35929951 PMCID: PMC9387110 DOI: 10.1021/acs.est.2c02207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Biocrusts covering drylands account for major fractions of terrestrial biological nitrogen fixation and release large amounts of gaseous reactive nitrogen (Nr) as nitrous acid (HONO) and nitric oxide (NO). Recent investigations suggested that aerobic and anaerobic microbial nitrogen transformations occur simultaneously upon desiccation of biocrusts, but the spatio-temporal distribution of seemingly contradictory processes remained unclear. Here, we explore small-scale gradients in chemical concentrations related to structural characteristics and organism distribution. X-ray microtomography and fluorescence microscopy revealed mixed pore size structures, where photoautotrophs and cyanobacterial polysaccharides clustered irregularly in the uppermost millimeter. Microsensor measurements showed strong gradients of pH, oxygen, and nitrite, nitrate, and ammonium ion concentrations at micrometer scales in both vertical and lateral directions. Initial oxygen saturation was mostly low (∼30%) at full water holding capacity, suggesting widely anoxic conditions, and increased rapidly upon desiccation. Nitrite concentrations (∼6 to 800 μM) and pH values (∼6.5 to 9.5) were highest around 70% WHC. During further desiccation they decreased, while emissions of HONO and NO increased, reaching maximum values around 20% WHC. Our results illustrate simultaneous, spatially separated aerobic and anaerobic nitrogen transformations, which are critical for Nr emissions, but might be impacted by future global change and land management.
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Affiliation(s)
- Alexandra Maria Kratz
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Stefanie Maier
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Jens Weber
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Minsu Kim
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Giacomo Mele
- Institute
for Agriculture and Forestry in the Mediterranean, National Council of Research, 80055 Portici, Italy
| | - Laura Gargiulo
- Institute
for Agriculture and Forestry in the Mediterranean, National Council of Research, 80055 Portici, Italy
| | - Anna Lena Leifke
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Maria Prass
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Raeid M. M. Abed
- College
of Science, Biology Department, Sultan Qaboos
University, P.O. Box 36, Al Khoud, Seeb 123, Sultanate of Oman
| | - Yafang Cheng
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Hang Su
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Ulrich Pöschl
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Bettina Weber
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
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15
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Choi RT, Reed SC, Tucker CL. Multiple resource limitation of dryland soil microbial carbon cycling on the Colorado Plateau. Ecology 2022; 103:e3671. [PMID: 35233760 DOI: 10.1002/ecy.3671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/20/2021] [Accepted: 11/11/2021] [Indexed: 11/06/2022]
Abstract
Understanding interactions among biogeochemical cycles is increasingly important as anthropogenic alterations of global climate and of carbon (C), nitrogen (N), and phosphorus (P) cycles interactively affect the Earth system. Ecosystem processes in the dryland biome, which makes up over 40% of Earth's terrestrial surface, are often distinctively sensitive to small changes in resource availability, likely because levels of many resources are low. However, data also suggest that simultaneous changes in the availability of multiple resources may be necessary to affect a response in these low-resource systems, offering an opportunity to test patterns and controls of co-limitation, serial limitation, and individual limitation in soil environments. While drylands may play a governing role in key aspects of Earth's C cycle, and while an improved understanding of resource limitation could substantially improve our forecasts of dryland responses to change, our understanding of interacting controls on soil C cycle processes remains notably poor in these dry systems. Here, we address multiple fundamental hypotheses of resource controls over ecosystem function to test how water, C, N, and P regulate soil C cycling individually and interactively in a dryland ecosystem on the Colorado Plateau. Using a series of laboratory incubations, we found that while water, C, and N limited C cycling through serial limitation, water alone resulted in an extremely small respiratory response from target organisms, whereas water + C resulted in a dramatic increase in soil C cycling, suggesting a degree of functional co-limitation. Nitrogen additions alone resulted in no changes to soil C cycling, but when N was added in concert with water and C, N greatly increased soil C cycling rates relative to additions of water and C without N. Phosphorus additions had no effect on the C cycle either alone or synergistically. These patterns were consistent with the stoichiometry of the system, and interactions among resources were surprising in ways that inform our understanding of critical theories in ecology, such as the Transient Maxima Hypothesis, supporting the suggestion that multiple resource limitation explains pulse-dynamic C cycling in drylands better than water limitation alone.
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Affiliation(s)
- Ryan T Choi
- Department of Wildland Resources, Utah State University and the Ecology Center, Logan, UT, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Colin L Tucker
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT, USA.,U.S.D.A Forest Service, Northern Research Station, Houghton, MI, USA
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16
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OUP accepted manuscript. Bioscience 2022. [DOI: 10.1093/biosci/biac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Miralles I, Trasar-Cepeda C, Soria R, Ortega R, Lucas-Borja ME. Environmental and ecological factors influencing soil functionality of biologically crusted soils by different lichen species in drylands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148491. [PMID: 34217081 DOI: 10.1016/j.scitotenv.2021.148491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/17/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Biocrusts are an essential soil surface cover at drylands where ecosystems are especially fragile to soil degradation processes due to climatic peculiarities. In the present work, (micro)biological and physicochemical properties indicative of soil functionality were studied in two different biocrust types dominated by Dipolschistes diacapsis and Lepraria isidiata and in underlying soil at two different depths (SL1, soil layer right below the biocrusts, and SL2, soil layer underlying SL1) at the Tabernas desert (southeast Spain). The influence of climatic factors (rainfall and temperature) and general soil properties on the (micro)biological properties were also analyzed in different environmental (climatic) conditions over a period of two years. PERMANOVA analyses showed significant statistical differences (Pseudo-F = 63.9; P (perm) = 0.001) among biocrust and soil layers. Throughout the study period, enzyme activities involved in C, N, and P cycles; microbial biomass-C; basal respiration; and several properties directly related to ecosystem productivity (total organic carbon, total nitrogen, concentration of ammonium and nitrate) were higher in both biocrust types than in the underlying soil layers, showing that biocrusts improved soil functions related to nutrient cycling. These properties progressively diminished in successive soil layers under the biocrusts (biocrusts > SL1 > SL2). Biocrusts showed greater similarity to each other and to SL1 than to SL2 in (micro)biological properties. A distance-based linear model analysis showed that total organic carbon, rainfall, pH, mineralized N-NH4+, and total nitrogen were the most important variables for predicting (micro)biological soil properties in biocrusts. Different biochemical behavior between the biocrusts and successive underlying soil layers has been found in wet periods. After rainfall periods, the biocrusts showed important peaks in basal soil respiration and in enzyme activities involved in C and P cycles. Nevertheless, soil biochemical properties hardly showed any peak in SL1 and did not change in SL2 despite soil moisture being higher in the soil layers below the biocrusts. Correlation analyses corroborated the existence of different relationships between soil moisture and enzymatic activities. In biocrusts, soil moisture showed a greater number of significant positive correlations with enzymes such as β-glucosidase, invertase, and phosphomonoesterase among others, whereas in SL1 it was only correlated with cellulase and in SL2 with dehydrogenase. A change in rainfall regime, as predicted by models based on climate change in arid and semiarid zones, could affect the activity of soil enzymes in the biocrusts and underlying layers, thus aggravating the degradation of these fragile dryland ecosystems.
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Affiliation(s)
- Isabel Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain.
| | - Carmen Trasar-Cepeda
- Departamento de Bioquímica del Suelo, Instituto de Investigaciones Agrobiológicas de Galicia, CSIC, Apartado 122, E-15780 Santiago de Compostela, Spain
| | - Rocío Soria
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - Raúl Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - Manuel Esteban Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, E-02071 Albacete, Spain
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18
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Ryan CH, Daly MG, Brady AL, Slater GF, Lim DSS. Organic Material Distribution in Mars-Analog Volcanic Rocks, as Determined with Ultraviolet Laser-Induced Fluorescence Spectroscopy. ASTROBIOLOGY 2021; 21:981-996. [PMID: 34406806 DOI: 10.1089/ast.2020.2379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding the distribution of trace organic material in a rocky environment is a key to constraining the material requirements for sustaining microbial life. We used an ultraviolet laser-induced fluorescence (LIF) spectroscopy instrument to characterize the distribution of organic biosignatures in basalts collected from two Mars-analog environments. We correlated the fluorescence results with alteration-related sample properties. These samples exhibit a range of alteration conditions found in the volcanic environments of Hawai'i Volcanoes National Park, Hawai'i (HI), and Craters of the Moon National Monument, Idaho (ID), including fumarolic systems. LIF mapping of the sample surfaces and interiors showed a heterogeneous distribution of areas of highly fluorescent material (point[s]-of-interest [POIs])-with fluorescence characteristics indicative of organic material. Results suggest that POIs are associated with secondary alteration mineral deposits in the rock's vesicles, including zeolites and calcite. Scanning electron microscopy with electron-dispersive X-ray spectroscopy was used to characterize the mineralogy present at POIs and support the evidence of carbon-bearing material. Overall, samples collected proximate to active or relict meteoric fumaroles from Hawai'i were shown to contain evidence for organic deposits. This suggests that these minerals are measurable spectroscopic targets that may be used to inform sample-site selection for astrobiology research.
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Affiliation(s)
- Catheryn H Ryan
- Centre for Research in Earth and Space Science, Lassonde School of Engineering, York University, Toronto, Canada
| | - Michael G Daly
- Centre for Research in Earth and Space Science, Lassonde School of Engineering, York University, Toronto, Canada
| | - Allyson L Brady
- School of Geography and Earth Sciences, McMaster University, Hamilton, Canada
| | - Greg F Slater
- National Aeronautics and Space Administration Ames Research Center, Moffett Field, California, USA
| | - Darlene S S Lim
- National Aeronautics and Space Administration Ames Research Center, Moffett Field, California, USA
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19
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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20
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Pombubpa N, Pietrasiak N, De Ley P, Stajich JE. Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA. FEMS Microbiol Ecol 2021; 96:5861315. [PMID: 32573682 DOI: 10.1093/femsec/fiaa125] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite there being extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface and subsurface soils at four sites located within the Mojave Desert. Five biocrust types were examined: Light-algal/Cyanobacteria, Cyanolichen, Green-algal lichen, Smooth-moss and Rough-moss crust types. Microbial diversity in biocrusts was structured by several characteristics: (i) central versus southern Mojave sites displayed different community signatures, (ii) indicator taxa of plant-associated fungi (plant pathogens and wood saprotrophs) were identified at each site, (iii) surface and subsurface microbial communities were distinct and (iv) crust types had distinct indicator taxa. Network analysis ranked bacteria-bacteria interactions as the most connected of all within-domain and cross-domain interaction networks in biocrust surface samples. Actinobacteria, Proteobacteria, Cyanobacteria and Ascomycota functioned as hubs among all phyla. The bacteria Pseudonocardia sp. (Pseudonocardiales, Actinobacteria) and fungus Alternaria sp. (Pleosporales, Ascomycota) were the most connected had the highest node degree. Our findings provide crucial insights for dryland microbial community ecology, conservation and sustainable management.
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Affiliation(s)
- Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521 USA
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM 88003, USA
| | - Paul De Ley
- Department of Nematology, University of California-Riverside, Riverside, CA 92521, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521 USA
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21
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Meier DV, Imminger S, Gillor O, Woebken D. Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. mSystems 2021; 6:e00786-20. [PMID: 33436509 PMCID: PMC7901476 DOI: 10.1128/msystems.00786-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.
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Affiliation(s)
- Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stefanie Imminger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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22
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Miralles I, Soria R, Lucas-Borja ME, Soriano M, Ortega R. Effect of biocrusts on bacterial community composition at different soil depths in Mediterranean semi-arid ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:138613. [PMID: 32446045 DOI: 10.1016/j.scitotenv.2020.138613] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
This study analyzed the influence of biocrusts on the chemical properties and bacterial diversity and community composition in the underlying soils along a depth gradient (the biocrust (C1), middle (S2) and deep (S3) soil layers) in two semi-arid Mediterranean ecosystems. Organic carbon, pH, electric conductivity and calcium carbonate content were estimated by wet oxidation, potentiometrically (pHmeter), with a conductivity-meter and volumetrically with a Bernard calcimeter, respectively. Bacterial diversity and community composition were estimated by 16S rRNA gene high-throughput amplicon sequencing. Chemical properties in C1 were significantly different from the other soil layers, showing higher organic carbon content and lower pH (p < 0.05). The relative abundance of several bacterial taxa, such as Bryocella, Methylobacterium, Segitebacter and Actinomycetospora showed significant positive correlations with organic carbon (r = 0.53 to 0.75) and negative with pH (r = -0.72 to -0.84), and were also highly correlated with each other (p < 0.01), suggesting a bacterial co-occurrence pattern associated with the biocrust. On the contrary, other bacterial taxa, such as Euzebyaceae, Truepera, Alphaproteobacteria and Caldinilaceae, showed positive correlations with electrical conductivity and calcium carbonate and were also correlated with each other (p < 0.01), in a second type of co-occurrence pattern associated with bare soil. The C1 and S2 layers had several taxa in common, while S3 layers had taxa common to bare soil, suggesting that the effect of biocrusts was limited to the first centimeters of soil and progressively decreased in depth. Bacterial diversity was lower in C1 than in the underlying layers and increased progressively from biocrust to deeper soil layers. The results suggest that the diversity and composition of soil microbial communities in biologically crusted sites in Mediterranean semi-arid environments are mainly controlled by chemical properties which in turn are modified by the biocrust along a depth gradient.
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Affiliation(s)
- I Miralles
- Department of Agronomy, University of Almeria, E-04120 Almería, Spain; Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain.
| | - R Soria
- Department of Agronomy, University of Almeria, E-04120 Almería, Spain; Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - M E Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071 Albacete, Spain
| | - M Soriano
- Department of Agronomy, University of Almeria, E-04120 Almería, Spain; Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - R Ortega
- Department of Agronomy, University of Almeria, E-04120 Almería, Spain; Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
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Amin A, Ahmed I, Khalid N, Khan IU, Ali A, Dahlawi SM, Li WJ. Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan. 3 Biotech 2020; 10:224. [PMID: 32373416 DOI: 10.1007/s13205-020-02204-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/10/2020] [Indexed: 11/30/2022] Open
Abstract
The present study was conducted to analyze bacterial diversity profile of Cholistan desert located in Pakistan. The study investigates the influence of physicochemical parameters of soil on distribution of different bacteria at all taxonomic levels and also study the distribution pattern between different desert environments, particularly rhizospheric and bulk desert sands. Species richness showed phyla Proteobacteria and Chloroflexi as the dominant OTUs in all the samples. Besides the two phyla, the rhizospheric soils with root remnants were dominated by Firmicutes, Deinococcus-Thermus, Actinobacteria and Acidobacteri, while phylum Thermotogae was present in significant quantity in rhizosheaths devoid of roots. In non-rhizospheric desert soils, a considerable number of OTUs belonged to phyla Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. An important finding from this study is that a bulk portion of the OTUs were assigned to unclassified taxa, indicating a large repertoire of unexplored taxa in the desert ecology of Pakistan. Distribution of taxonomic groups among various regions of the desert was collaborating well with the physicochemical parameters of the sites. The findings of this study establish the fundamental relationships between desert ecosystem, specific native plant and the total bacterial flora. This is the first study of microbial community analysis of any desert in Pakistan and thus, will serve as a future platform to explore further on desert ecosystem functioning by employing the ever-changing biotechnological tools.
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Affiliation(s)
- Arshia Amin
- 1State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People's Republic of China
- 2National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, 45500 Pakistan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 45500 Pakistan
| | - Iftikhar Ahmed
- 2National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, 45500 Pakistan
| | - Nauman Khalid
- 4School of Food and Agricultural Sciences, University of Management and Technology, Lahore, 54000 Pakistan
| | - Inam Ullah Khan
- 5Institute of Microbiology, Faculty of Veterinary and Animal Sciences,, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ahmad Ali
- 2National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, 45500 Pakistan
| | - Saad Mohammad Dahlawi
- 6Department of Environmental Health, College of Public Health, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Wen-Jun Li
- 1State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People's Republic of China
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Ayuso SV, Giraldo‐Silva A, Barger NN, Garcia‐Pichel F. Microbial inoculum production for biocrust restoration: testing the effects of a common substrate versus native soils on yield and community composition. Restor Ecol 2020. [DOI: 10.1111/rec.13127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Sergio Velasco Ayuso
- School of Life SciencesArizona State University Tempe AZ 85287 U.S.A
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA‐CONICET), Facultad de Agronomía, Universidad de Buenos Aires Buenos Aires C1417DSE Argentina
| | - Ana Giraldo‐Silva
- School of Life SciencesArizona State University Tempe AZ 85287 U.S.A
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State University Tempe AZ 85287 U.S.A
| | - Nichole N. Barger
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO 80309 U.S.A
| | - Ferran Garcia‐Pichel
- School of Life SciencesArizona State University Tempe AZ 85287 U.S.A
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State University Tempe AZ 85287 U.S.A
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Reed SC, Delgado-Baquerizo M, Ferrenberg S. Biocrust science and global change. THE NEW PHYTOLOGIST 2019; 223:1047-1051. [PMID: 31304606 DOI: 10.1111/nph.15992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Sasha C Reed
- US Geological Survey, Southwest Biological Science Center, Moab, UT, 84532, USA
| | - Manuel Delgado-Baquerizo
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Calle Tulipán Sin Número, Móstoles, 28933, Spain
| | - Scott Ferrenberg
- Department of Biology, New Mexico State University, Las Cruces, NM, 88001, USA
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Kaur S, Kurtz HD. Core bacterial community composition of a cryptoendolithic ecosystem in the Grand Staircase-Escalante National Monument, Utah. Microbiologyopen 2019; 8:e00707. [PMID: 30079546 PMCID: PMC6528646 DOI: 10.1002/mbo3.707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/12/2018] [Accepted: 07/04/2018] [Indexed: 11/21/2022] Open
Abstract
Cryptoendolithic bacterial communities in the Jurassic Navajo Sandstones play an important ecological role in this ecosystem. Developing a better understanding of the role of these cryptoendolithic communities required a deeper knowledge of the microbial diversity present. We analyzed the bacterial diversity in eight sandstones samples from several microgeological features associated with a large sandstone dome. Cryptoendolithic bacterial diversity is clustered into three distinct groups which correlated with topography, suggesting the duration of water retention might be a factor. Comparisons of diversity between each cluster showed that a core bacterial community exists in this habitat. The overall bacterial community structure was dominated by Cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria. The most prevalent genera in cyanobacteria were Leptolyngbya, Chroococcidiopsis, and unclassified cyanobacteria accounting for the bulk of cyanobacterial sequences. Within the Proteobacteria, Alphaproteobacteria were the largest class detected, with members of the Acetobacteraceae, particularly the genus Acidiphilium, being the most abundant. Acidiphilium spp. are capable of aerobic ferric iron reduction under moderately acidic conditions, explaining the high levels of iron (II) in this system. This study highlights the extent of unexplored bacterial diversity in this habitat system and sets the premise for elaborating on the ecological function of cryptoendolithic communities.
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Affiliation(s)
- Sukhpreet Kaur
- Department of Biological SciencesClemson UniversityClemsonSouth Carolina
| | - HD Kurtz
- Department of Biological SciencesClemson UniversityClemsonSouth Carolina
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Cockell CS, Harrison JP, Stevens AH, Payler SJ, Hughes SS, Kobs Nawotniak SE, Brady AL, Elphic R, Haberle CW, Sehlke A, Beaton KH, Abercromby AF, Schwendner P, Wadsworth J, Landenmark H, Cane R, Dickinson AW, Nicholson N, Perera L, Lim DS. A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars. ASTROBIOLOGY 2019; 19:284-299. [PMID: 30840501 PMCID: PMC6442273 DOI: 10.1089/ast.2018.1870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai'i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai'i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.
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Affiliation(s)
- Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- Address correspondence to: Charles S. Cockell, School of Physics and Astronomy, University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
| | - Jesse P. Harrison
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Adam H. Stevens
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Samuel J. Payler
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Scott S. Hughes
- Department of Geosciences, Idaho State University, Pocatello, Idaho, USA
| | | | - Allyson L. Brady
- School of Geography and Earth Sciences, McMaster University, Hamilton, Canada
| | - R.C. Elphic
- NASA Ames Research Center, Mountain View, California, USA
| | | | | | | | - Andrew F.J. Abercromby
- Biomedical Research & Environmental Sciences Division (SK), NASA Johnson Space Center, Houston, Texas, USA
| | - Petra Schwendner
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Jennifer Wadsworth
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Hanna Landenmark
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Rosie Cane
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Andrew W. Dickinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Natasha Nicholson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Liam Perera
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Darlene S.S. Lim
- NASA Ames Research Center, Mountain View, California, USA
- Bay Area Environmental Research Institute (BAERI), Moffett Field, California, USA
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Ma J, Bei Q, Wang X, Lan P, Liu G, Lin X, Liu Q, Lin Z, Liu B, Zhang Y, Jin H, Hu T, Zhu J, Xie Z. Impacts of Mo application on biological nitrogen fixation and diazotrophic communities in a flooded rice-soil system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:686-694. [PMID: 30176479 DOI: 10.1016/j.scitotenv.2018.08.318] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 05/27/2023]
Abstract
Molybdenum (Mo) deficiency in the farmland of China may limit biological nitrogen fixation (BNF), however, the impact of Mo application on BNF capacities and diazotrophic communities in rice-soil systems is unclear. In this experiment, treatments in a 6.7 atom% 15N2-labelling field-based growth chamber for 74 days and treatments in a 99 atom% 15N2-labelling microcosm experiment for 40 days combined with 16S rRNA gene sequencing and DNA-stable isotope probing (SIP) were used to investigate the impacts of Mo application on BNF and diazotrophic communities. Our results showed that under the condition that no nitrogen (N) fertilizer was applied, Mo application (500 g sodium molybdate ha-1) significantly increased N2 fixation in a rice-Inceptisol system, from 22.3 to 53.1 kg N ha-1. Mo application significantly increased the number of nifH gene copies and the relative abundance of cyanobacteria in both growth chamber and microcosm experiments. Among cyanobacteria, the relative abundances of the most abundant genera Leptolyngbya and Microcoleus were significantly increased by Mo application. 15N2-DNA-SIP further demonstrated that Leptolyngbya and Microcoleus incorporated 15N2. Mo application greatly increased BNF in Mo-deficient paddy field (≤0.068 mg kg-1) and stimulated the growth of cyanobacteria. These results indicated that Mo application in Mo-deficient paddy field could be a useful measure to increase soil N input under no N fertilization.
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Affiliation(s)
- Jing Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Qicheng Bei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China
| | - Xiaojie Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China
| | - Gang Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China
| | - Xingwu Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China
| | - Qi Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Zhibin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Benjuan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Yanhui Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Haiyang Jin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Tianlong Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China; University of Chinese Academy of Sciences, Yuquan Road No. 19A, Beijing 100049, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China
| | - Zubin Xie
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing 210008, China.
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Steven B, Belnap J, Kuske CR. Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing. Front Microbiol 2018; 9:2382. [PMID: 30349515 PMCID: PMC6186815 DOI: 10.3389/fmicb.2018.02382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Biological soil crusts (biocrusts) are microbial communities that are a feature of arid surface soils worldwide. In drylands where precipitation is pulsed and ephemeral, the ability of biocrust microbiota to rapidly initiate metabolic activity is critical to their survival. Community gene expression was compared after a short duration (1 h) wetting pulse in both intact and soils disturbed by chronic foot trampling. Across the metatranscriptomes the majority of transcripts were cyanobacterial in origin, suggesting that cyanobacteria accounted for the bulk of the transcriptionally active cells. Chronic trampling substantially altered the functional profile of the metatranscriptomes, specifically resulting in a significant decrease in transcripts for nitrogen fixation. Soil depth (biocrust and below crust) was a relatively small factor in differentiating the metatranscriptomes, suggesting that the metabolically active bacteria were similar between shallow soil horizons. The dry samples were consistently enriched for hydrogenase genes, indicating that molecular hydrogen may serve as an energy source for the desiccated soil communities. The water pulse was associated with a restructuring of the metatranscriptome, particularly for the biocrusts. Biocrusts increased transcripts for photosynthesis and carbon fixation, suggesting a rapid resuscitation upon wetting. In contrast, the trampled surface soils showed a much smaller response to wetting, indicating that trampling altered the metabolic response of the community. Finally, several biogeochemical cycling genes in carbon and nitrogen cycling were assessed for their change in abundance due to wetting in the biocrusts. Different transcripts encoding the same gene product did not show a consensus response, with some more abundant in dry or wet biocrusts, highlighting the challenges in relating transcript abundance to biogeochemical cycling rates. These observations demonstrate that metatranscriptome sequencing was able to distinguish alterations in the function of arid soil microbial communities at two varying temporal scales, a long-term ecosystems disturbance through foot trampling, and a short term wetting pulse. Thus, community metatranscriptomes have the potential to inform studies on the response and resilience of biocrusts to various environmental perturbations.
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Affiliation(s)
- Blaire Steven
- Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, CT, United States
| | - Jayne Belnap
- Southwest Biological Science Center, United States Geological Survey, Moab, UT, United States
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Tucker CL, Ferrenberg S, Reed SC. Climatic Sensitivity of Dryland Soil CO2 Fluxes Differs Dramatically with Biological Soil Crust Successional State. Ecosystems 2018. [DOI: 10.1007/s10021-018-0250-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Large Blooms of Bacillales ( Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity. mBio 2018; 9:mBio.01366-16. [PMID: 29511079 PMCID: PMC5844995 DOI: 10.1128/mbio.01366-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological soil crusts (biocrusts) account for a substantial portion of primary production in dryland ecosystems. They successionally mature to deliver a suite of ecosystem services, such as carbon sequestration, water retention and nutrient cycling, and climate regulation. Biocrust assemblages are extremely well adapted to survive desiccation and to rapidly take advantage of the periodic precipitation events typical of arid ecosystems. Here we focus on the wetting response of incipient cyanobacterial crusts as they mature from "light" to "dark." We sampled a cyanobacterial biocrust chronosequence before (dry) and temporally following a controlled wetting event and used high-throughput 16S rRNA and rRNA gene sequencing to monitor the dynamics of microbial response. Overall, shorter-term changes in phylogenetic beta diversity attributable to periodic wetting were as large as those attributable to biocrust successional stage. Notably, more mature crusts showed significantly higher resistance to precipitation disturbance. A large bloom of a few taxa within the Firmicutes, primarily in the order Bacillales, emerged 18 h after wetting, while filamentous crust-forming cyanobacteria showed variable responses to wet-up across the successional gradient, with populations collapsing in less-developed light crusts but increasing in later-successional-stage dark crusts. Overall, the consistent Bacillales bloom accompanied by the variable collapse of pioneer cyanobacteria of the Oscillatoriales order across the successional gradient suggests that the strong response of few organisms to a hydration pulse with the mortality of the autotroph might have important implications for carbon (C) balance in semiarid ecosystems.IMPORTANCE Desert biological soil crusts are terrestrial topsoil microbial communities common to arid regions that comprise 40% of Earth's terrestrial surface. They successionally develop over years to decades to deliver a suite of ecosystem services of local and global significance. Ecosystem succession toward maturity has been associated with both resistance and resilience to disturbance. Recent work has shown that the impacts of both climate change and physical disturbance on biocrusts increase the potential for successional resetting. A larger proportion of biocrusts are expected to be at an early developmental stage, hence increasing susceptibility to changes in precipitation frequencies. Therefore, it is essential to characterize how biocrusts respond to wetting across early developmental stages. In this study, we document the wetting response of microbial communities from a biocrust chronosequence. Overall, our results suggest that the cumulative effects of altered precipitation frequencies on the stability of biocrusts will depend on biocrust maturity.
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Maier S, Tamm A, Wu D, Caesar J, Grube M, Weber B. Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. ISME JOURNAL 2018; 12:1032-1046. [PMID: 29445133 PMCID: PMC5864206 DOI: 10.1038/s41396-018-0062-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/21/2017] [Accepted: 01/10/2018] [Indexed: 01/10/2023]
Abstract
Biological soil crusts (biocrusts) cover about 12% of the Earth’s land masses, thereby providing ecosystem services and affecting biogeochemical fluxes on a global scale. They comprise photoautotrophic cyanobacteria, algae, lichens and mosses, which grow together with heterotrophic microorganisms, forming a model system to study facilitative interactions and assembly principles in natural communities. Biocrusts can be classified into cyanobacteria-, lichen-, and bryophyte-dominated types, which reflect stages of ecological succession. In this study, we examined whether these categories include a shift in heterotrophic communities and whether this may be linked to altered physiological properties. We analyzed the microbial community composition by means of qPCR and high-throughput amplicon sequencing and utilized flux measurements to investigate their physiological properties. Our results revealed that once 16S and 18S rRNA gene copy numbers increase, fungi become more predominant and alpha diversity increases with progressing succession. Bacterial communities differed significantly between biocrust types with a shift from more generalized to specialized organisms along succession. CO2 gas exchange measurements revealed large respiration rates of late successional crusts being significantly higher than those of initial biocrusts, and different successional stages showed distinct NO and HONO emission patterns. Thus, our study suggests that the photoautotrophic organisms facilitate specific microbial communities, which themselves strongly influence the overall physiological properties of biocrusts and hence local to global nutrient cycles.
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Affiliation(s)
- Stefanie Maier
- Max Planck Institute for Chemistry, Multiphase Chemistry, Mainz, Germany.
| | - Alexandra Tamm
- Max Planck Institute for Chemistry, Multiphase Chemistry, Mainz, Germany
| | - Dianming Wu
- Max Planck Institute for Chemistry, Multiphase Chemistry, Mainz, Germany.,Key Laboratory of Geographic Information Sciences, Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Jennifer Caesar
- Department of Agriculture & Food Sciences, University of Applied Sciences, Neubrandenburg, Germany
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | - Bettina Weber
- Max Planck Institute for Chemistry, Multiphase Chemistry, Mainz, Germany.
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Garibotti IA, Gonzalez Polo M, Tabeni S. Linking biological soil crust attributes to the multifunctionality of vegetated patches and interspaces in a semiarid shrubland. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Irene A. Garibotti
- Instituto de Investigaciones en Biodiversidad y MedioambienteUniversidad Nacional del ComahueCONICET Bariloche Argentina
| | - Marina Gonzalez Polo
- Instituto de Investigaciones en Biodiversidad y MedioambienteUniversidad Nacional del ComahueCONICET Bariloche Argentina
| | - Solana Tabeni
- Instituto Argentino de Investigaciones de las Zonas ÁridasUniversidad Nacional de CuyoCONICET Mendoza Argentina
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Fernandes VMC, Machado de Lima NM, Roush D, Rudgers J, Collins SL, Garcia-Pichel F. Exposure to predicted precipitation patterns decreases population size and alters community structure of cyanobacteria in biological soil crusts from the Chihuahuan Desert. Environ Microbiol 2017; 20:259-269. [PMID: 29124873 DOI: 10.1111/1462-2920.13983] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/16/2017] [Accepted: 11/02/2017] [Indexed: 11/29/2022]
Abstract
Cyanobacteria typically colonize the surface of arid soils, building biological soil crust (biocrusts) that provide a variety of ecosystem benefits, ranging from fertilization to stabilization against erosion. We investigated how future scenarios in precipitation anticipated for the Northern Chihuahuan Desert affected abundance and composition of biocrust cyanobacteria in two grassland ecosystems. Scenarios included a decrease in precipitation and a delay of monsoon rainfall. After three years, both treatments negatively affected cyanobacteria, although the effects of monsoon delay were milder than those of decreased precipitation. Mature biocrusts in black grama grassland suffered severe losses in cyanobacterial biomass and diversity, but compositionally simpler biocrusts in blue grama-dominated grassland maintained biomass, only suffering diversity losses. This could be partially explained by the differential sensitivity of cyanobacterial taxa: nitrogen-fixing Scytonema spp. were the most sensitive, followed by phylotypes in the Microcoleus steenstrupii complex. Microcoleus vaginatus was the least affected in all cases, but is known to be very sensitive to warming. We predict that altered precipitation will tend to prevent biocrusts from reaching successional maturity, selecting for M. vaginatus over competing M. steenstrupii, among pioneer biocrust-formers. A shift towards heat-sensitive M. vaginatus could ultimately destabilize biocrusts when precipitation changes are combined with global warming.
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Affiliation(s)
- Vanessa M C Fernandes
- School of Life Sciences and Center for Applied and Fundamental Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | | | - Daniel Roush
- School of Life Sciences and Center for Applied and Fundamental Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Jennifer Rudgers
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Scott L Collins
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ferran Garcia-Pichel
- School of Life Sciences and Center for Applied and Fundamental Microbiomics, Arizona State University, Tempe, AZ 85287, USA
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Bar Eyal L, Ranjbar Choubeh R, Cohen E, Eisenberg I, Tamburu C, Dorogi M, Ünnep R, Appavou MS, Nevo R, Raviv U, Reich Z, Garab G, van Amerongen H, Paltiel Y, Keren N. Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria. Proc Natl Acad Sci U S A 2017; 114:9481-9486. [PMID: 28808031 PMCID: PMC5584450 DOI: 10.1073/pnas.1708206114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In this paper we propose an energy dissipation mechanism that is completely reliant on changes in the aggregation state of the phycobilisome light-harvesting antenna components. All photosynthetic organisms regulate the efficiency of excitation energy transfer (EET) to fit light energy supply to biochemical demands. Not many do this to the extent required of desert crust cyanobacteria. Following predawn dew deposition, they harvest light energy with maximum efficiency until desiccating in the early morning hours. In the desiccated state, absorbed energy is completely quenched. Time and spectrally resolved fluorescence emission measurements of the desiccated desert crust Leptolyngbya ohadii strain identified (i) reduced EET between phycobilisome components, (ii) shorter fluorescence lifetimes, and (iii) red shift in the emission spectra, compared with the hydrated state. These changes coincide with a loss of the ordered phycobilisome structure, evident from small-angle neutron and X-ray scattering and cryo-transmission electron microscopy data. Based on these observations we propose a model where in the hydrated state the organized rod structure of the phycobilisome supports directional EET to reaction centers with minimal losses due to thermal dissipation. In the desiccated state this structure is lost, giving way to more random aggregates. The resulting EET path will exhibit increased coupling to the environment and enhanced quenching.
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Affiliation(s)
- Leeat Bar Eyal
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Reza Ranjbar Choubeh
- Laboratory of Biophysics, Wageningen University, 6700 ET Wageningen, The Netherlands
| | - Eyal Cohen
- Applied Physics Department, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ido Eisenberg
- Applied Physics Department, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Carmen Tamburu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Márta Dorogi
- Biological Research Centre, Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Renata Ünnep
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, H-1525 Budapest 114, Hungary
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ziv Reich
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600, Israel
| | - Győző Garab
- Biological Research Centre, Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Herbert van Amerongen
- Laboratory of Biophysics, Wageningen University, 6700 ET Wageningen, The Netherlands
| | - Yossi Paltiel
- Applied Physics Department, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nir Keren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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Andrade AC, Fróes A, Lopes FÁC, Thompson FL, Krüger RH, Dinsdale E, Bruce T. Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome. MICROBIAL ECOLOGY 2017; 74:89-105. [PMID: 28070679 DOI: 10.1007/s00248-016-0911-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.
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Affiliation(s)
- Ana Camila Andrade
- Faculdade de Tecnologia e Ciências, Grupo de Biotecnologia Ambiental, Department of Bioenergy, Salvador, Brazil
| | - Adriana Fróes
- Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | - Thiago Bruce
- Faculdade de Tecnologia e Ciências, Grupo de Biotecnologia Ambiental, Department of Bioenergy, Salvador, Brazil.
- Department of Biology, San Diego State University, San Diego, CA, USA.
- Institute of Biology, Microbiology department, Universidade Federal da Bahia (UFBA), Rio de Janeiro, Brazil.
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Velasco Ayuso S, Giraldo Silva A, Nelson C, Barger NN, Garcia-Pichel F. Microbial Nursery Production of High-Quality Biological Soil Crust Biomass for Restoration of Degraded Dryland Soils. Appl Environ Microbiol 2017; 83:e02179-16. [PMID: 27864178 PMCID: PMC5244311 DOI: 10.1128/aem.02179-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/15/2016] [Indexed: 11/20/2022] Open
Abstract
Biological soil crusts (biocrusts) are slow-growing, phototroph-based microbial assemblages that develop on the topsoils of drylands. Biocrusts help maintain soil fertility and reduce erosion. Because their loss through human activities has negative ecological and environmental health consequences, biocrust restoration is of interest. Active soil inoculation with biocrust microorganisms can be an important tool in this endeavor. We present a culture-independent, two-step process to grow multispecies biocrusts in open greenhouse nursery facilities, based on the inoculation of local soils with local biocrust remnants and incubation under seminatural conditions that maintain the essence of the habitat but lessen its harshness. In each of four U.S. Southwest sites, we tested and deployed combinations of factors that maximized growth (gauged as chlorophyll a content) while minimizing microbial community shifts (assessed by 16S rRNA sequencing and bioinformatics), particularly for crust-forming cyanobacteria. Generally, doubling the frequency of natural wetting events, a 60% reduction in sunlight, and inoculation by slurry were optimal. Nutrient addition effects were site specific. In 4 months, our approach yielded crusts of high inoculum quality reared on local soil exposed to locally matched climates, acclimated to desiccation, and containing communities minimally shifted in composition from local ones. Our inoculum contained abundant crust-forming cyanobacteria and no significant numbers of allochthonous phototrophs, and it was sufficient to treat ca. 6,000 m2 of degraded dryland soils at 1 to 5% of the typical crust biomass concentration, having started from a natural crust remnant as small as 6 to 30 cm2 IMPORTANCE: Soil surface crusts can protect dryland soils from erosion, but they are often negatively impacted by human activities. Their degradation causes a loss of fertility, increased production of fugitive dust and intensity of dust storms with associated traffic problems, and provokes general public health hazards. Our results constitute an advance in the quest to actively restore biological soil covers by providing a means to obtain high-quality inoculum within a reasonable time (a few months), thereby allowing land managers to recover essential, but damaged, ecosystem services in a sustainable, self-perpetuating way as provided by biocrust communities.
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Affiliation(s)
| | - Ana Giraldo Silva
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Corey Nelson
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Nichole N Barger
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Bates ST, Nash TH, Garcia-Pichel F. Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States. Mycologia 2017; 104:353-61. [PMID: 22123652 DOI: 10.3852/11-232] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Scott T. Bates
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309
| | - Thomas H. Nash
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, Arizona 85287-4501
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, Arizona 85287-4501
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Porras-Alfaro A, Herrera J, Natvig DO, Lipinski K, Sinsabaugh RL. Diversity and distribution of soil fungal communities in a semiarid grassland. Mycologia 2017; 103:10-21. [DOI: 10.3852/09-297] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andrea Porras-Alfaro
- Department of Biological Sciences, Waggoner Hall 372, 1 University Circle, Western Illinois University, Macomb, Illinois 61455
| | - Jose Herrera
- Department of Biology, 100 E. Normal, Truman State University, Kirksville, Missouri 63501
| | | | | | - Robert L. Sinsabaugh
- Department of Biology, MSC03 2020, University of New Mexico at Albuquerque, New Mexico 87131-0001
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41
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Zhou X, Smith H, Giraldo Silva A, Belnap J, Garcia-Pichel F. Differential Responses of Dinitrogen Fixation, Diazotrophic Cyanobacteria and Ammonia Oxidation Reveal a Potential Warming-Induced Imbalance of the N-Cycle in Biological Soil Crusts. PLoS One 2016; 11:e0164932. [PMID: 27776160 PMCID: PMC5077114 DOI: 10.1371/journal.pone.0164932] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023] Open
Abstract
N2 fixation and ammonia oxidation (AO) are the two most important processes in the nitrogen (N) cycle of biological soil crusts (BSCs). We studied the short-term response of acetylene reduction assay (ARA) rates, an indicator of potential N2 fixation, and AO rates to temperature (T, -5°C to 35°C) in BSC of different successional stages along the BSC ecological succession and geographic origin (hot Chihuahuan and cooler Great Basin deserts). ARA in all BSCs increased with T until saturation occurred between 15 and 20°C, and declined at 30-35°C. Culture studies using cyanobacteria isolated from these crusts indicated that the saturating effect was traceable to their inability to grow well diazotrophically within the high temperature range. Below saturation, temperature response was exponential, with Q10 significantly different in the two areas (~ 5 for Great Basin BSCs; 2-3 for Chihuahuan BSCs), but similar between the two successional stages. However, in contrast to ARA, AO showed a steady increase to 30-35°C in Great Basin, and Chihuhuan BSCs showed no inhibition at any tested temperature. The T response of AO also differed significantly between Great Basin (Q10 of 4.5-4.8) and Chihuahuan (Q10 of 2.4-2.6) BSCs, but not between successional stages. Response of ARA rates to T did not differ from that of AO in either desert. Thus, while both processes scaled to T in unison until 20°C, they separated to an increasing degree at higher temperature. As future warming is likely to occur in the regions where BSCs are often the dominant living cover, this predicted decoupling is expected to result in higher proportion of nitrates in soil relative to ammonium. As nitrate is more easily lost as leachate or to be reduced to gaseous forms, this could mean a depletion of soil N over large landscapes globally.
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Affiliation(s)
- Xiaobing Zhou
- Arizona State University, School of Life Sciences,Tempe, AZ 85287, United States of America
- Xinjiang Institute of Ecology and Geography, Key Laboratory of Biogeography and Bioresource in Arid Land, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Hilda Smith
- U. S. Geological Survey, Southwest Biological Science Center, Moab, UT 84532, United States of America
| | - Ana Giraldo Silva
- Arizona State University, School of Life Sciences,Tempe, AZ 85287, United States of America
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States of America
| | - Jayne Belnap
- U. S. Geological Survey, Southwest Biological Science Center, Moab, UT 84532, United States of America
| | - Ferran Garcia-Pichel
- Arizona State University, School of Life Sciences,Tempe, AZ 85287, United States of America
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States of America
- * E-mail:
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42
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Aslam SN, Dumbrell AJ, Sabir JS, Mutwakil MHZ, Baeshen MMN, Abo-Aba SEM, Clark DR, Yates SA, Baeshen NA, Underwood GJC, McGenity TJ. Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota. Environ Microbiol 2016; 18:5048-5062. [PMID: 27459511 DOI: 10.1111/1462-2920.13474] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Although desert soils support functionally important microbial communities that affect plant growth and influence many biogeochemical processes, the impact of future changes in precipitation patterns on the microbiota and their activities is largely unknown. We performed in-situ experiments to investigate the effect of simulated rainfall on bacterial communities associated with the widespread perennial shrub, Rhazya stricta in Arabian desert soils. The bacterial community composition was distinct between three different soil compartments: surface biological crust, root-attached, and the broader rhizosphere. Simulated rainfall had no significant effect on the overall bacterial community composition, but some population-level responses were observed, especially in soil crusts where Betaproteobacteria, Sphingobacteria, and Bacilli became more abundant. Bacterial biomass in the nutrient-rich crust increased three-fold one week after watering, whereas it did not change in the rhizosphere, despite its much higher water retention. These findings indicate that between rainfall events, desert-soil microbial communities enter into stasis, with limited species turnover, and reactivate rapidly and relatively uniformly when water becomes available. However, microbiota in the crust, which was relatively enriched in nutrients and organic matter, were primarily water-limited, compared with the rhizosphere microbiota that were co-limited by nutrients and water.
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Affiliation(s)
- Shazia N Aslam
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Alex J Dumbrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Jamal S Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed H Z Mutwakil
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammed M N Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Salah E M Abo-Aba
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Dave R Clark
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Steven A Yates
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Graham J C Underwood
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
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Effect of Different Broad Waveband Lights on Membrane Lipids of a Cyanobacterium, Synechococcus sp., as Determined by UPLC-QToF-MS and Vibrational Spectroscopy. BIOLOGY 2016; 5:biology5020022. [PMID: 27223306 PMCID: PMC4929536 DOI: 10.3390/biology5020022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 11/17/2022]
Abstract
Differential profile of membrane lipids and pigments of a Synechococcus sp. cyanobacterial strain cells exposed to blue, green, red and white light are determined by means of liquid chromatography and mass spectrometry or diode array detection. Raman and ATR-IR spectra of intact cells under the diverse light wavebands are also reported. Blue light cells exhibited an increased content of photosynthetic pigments as well as specific species of membrane glycerolipids as compared to cells exposed to other wavebands. The A630/A680 ratio indicated an increased content of phycobilisomes (PBS) in the blue light-exposed cells. Some differences in the protein conformation between the four light waveband-exposed cells were deduced from the variable absorbance at specific wavenumbers in the FT-Raman and ATR-FTIR spectra, in particular bands assigned to amide I and amide II. Bands from 1180 to 950 cm(-1) in the ATR-FTIR spectrum suggest degraded outer membrane polysaccharide in the blue light-exposed cells.
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44
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Zhang B, Kong W, Wu N, Zhang Y. Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China. J Basic Microbiol 2016; 56:670-9. [PMID: 26947139 DOI: 10.1002/jobm.201500751] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/06/2016] [Indexed: 11/11/2022]
Abstract
Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as Sphingomonas sp. Niastella sp., Pedobacter, and Candidatus solobacter increased. Therefore, bacterial community composition and their key ecological roles shifted to the development of BSCs.
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Affiliation(s)
- Bingchang Zhang
- Key Laboratory of Biogeography and Bioresources in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Nan Wu
- Key Laboratory of Biogeography and Bioresources in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yuanming Zhang
- Key Laboratory of Biogeography and Bioresources in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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45
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Pepe-Ranney C, Koechli C, Potrafka R, Andam C, Eggleston E, Garcia-Pichel F, Buckley DH. Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation. THE ISME JOURNAL 2016; 10:287-98. [PMID: 26114889 PMCID: PMC4737922 DOI: 10.1038/ismej.2015.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 11/08/2022]
Abstract
Biological soil crusts (BSCs) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface. In particular, BSC N2-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems. In mature crusts, N2-fixation is largely attributed to heterocystous cyanobacteria; however, early successional crusts possess few N2-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development. DNA stable isotope probing with (15)N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate (15)N2 in early successional crusts. The Clostridiaceae identified are divergent from previously characterized isolates, though N2-fixation has previously been observed in this family. The Proteobacteria identified share >98.5% small subunit rRNA gene sequence identity with isolates from genera known to possess diazotrophs (for example, Pseudomonas, Klebsiella, Shigella and Ideonella). The low abundance of these heterotrophic diazotrophs in BSCs may explain why they have not been characterized previously. Diazotrophs have a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSCs in arid ecosystems.
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Affiliation(s)
- Charles Pepe-Ranney
- Department of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Chantal Koechli
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Ruth Potrafka
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Cheryl Andam
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Erin Eggleston
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Daniel H Buckley
- Department of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
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Zhu T, Dittrich M. Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review. Front Bioeng Biotechnol 2016; 4:4. [PMID: 26835451 PMCID: PMC4718973 DOI: 10.3389/fbioe.2016.00004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/07/2016] [Indexed: 11/24/2022] Open
Abstract
Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.
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Affiliation(s)
- Tingting Zhu
- Department of Physical and Environmental Sciences, University of Toronto Scarborough , Toronto, ON , Canada
| | - Maria Dittrich
- Department of Physical and Environmental Sciences, University of Toronto Scarborough , Toronto, ON , Canada
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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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48
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Mueller RC, Belnap J, Kuske CR. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland. Front Microbiol 2015; 6:891. [PMID: 26388845 PMCID: PMC4559666 DOI: 10.3389/fmicb.2015.00891] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 or 0-10 cm) across the N-amendment gradient (0, 7, and 15 kg ha(-1) yr(-1)). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.
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Affiliation(s)
- Rebecca C Mueller
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Jayne Belnap
- Southwest Biological Science Center, United States Geological Survey Moab, UT, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
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49
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Raanan H, Oren N, Treves H, Berkowicz SM, Hagemann M, Pade N, Keren N, Kaplan A. Simulated soil crust conditions in a chamber system provide new insights on cyanobacterial acclimation to desiccation. Environ Microbiol 2015; 18:414-26. [PMID: 26234786 DOI: 10.1111/1462-2920.12998] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Environmental research often faces two major hurdles: (i) fluctuating spatial and temporal conditions and consequently large variability in the organisms' abundance and performance, and (ii) complex, costly logistics involved in field experiments. Measurements of physiological parameters or molecular analyses often represent single shot experiments. To study desiccation acclimation of filamentous cyanobacteria, the founders and main primary producers in desert biological soil crusts (BSC), we constructed an environmental chamber that can reproducibly and accurately simulate ambient conditions and measure microorganism performance. We show that recovery from desiccation of BSC cyanobacteria and Leptolyngbya ohadii isolated thereof are strongly affected by dehydration rate following morning dew. This effect is most pronounced in cells exposed to high light and temperature in the dry phase. Simultaneous measurements of water content, gas exchange and fluorescence were performed during dehydration. Photosynthetic performance measured by fluorescence begins declining when light intensity reaches values above 100 μmol photons m(-2) s(-1), even in fully hydrated cells. In contrast, photosynthetic rates measured using O2 evolution and CO2 uptake increased during rising irradiance to the point where the water content declined below ∼ 50%. Thus, fluorescence cannot serve as a reliable measure of photosynthesis in desert cyanobacteria. The effects of drying on gas exchange are discussed.
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Affiliation(s)
- Hagai Raanan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Nadav Oren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Haim Treves
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Simon M Berkowicz
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.,Arid Ecosystems Research Center, Edmond J. Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem, 91904, 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
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.,Arid Ecosystems Research Center, Edmond J. Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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50
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Raanan H, Felde VJMNL, Peth S, Drahorad S, Ionescu D, Eshkol G, Treves H, Felix-Henningsen P, Berkowicz SM, Keren N, Horn R, Hagemann M, Kaplan A. Three-dimensional structure and cyanobacterial activity within a desert biological soil crust. Environ Microbiol 2015; 18:372-83. [DOI: 10.1111/1462-2920.12859] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/26/2015] [Accepted: 03/06/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Hagai Raanan
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Vincent J. M. N. L. Felde
- Institute of Soil Science and Soil Conservation; Justus Liebig University Giessen; 35392 Giessen Germany
| | - Stephan Peth
- Deparment of Soil Science; Faculty of Ecological Agriculture; University of Kassel; 37213 Witzenhausen Germany
| | - Sylvie Drahorad
- Institute of Soil Science and Soil Conservation; Justus Liebig University Giessen; 35392 Giessen Germany
| | - Danny Ionescu
- The Max Planck Institute for Marine Microbiology; Celsius Str. 1 28359 Bremen Germany
| | - Gil Eshkol
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Haim Treves
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Peter Felix-Henningsen
- Institute of Soil Science and Soil Conservation; Justus Liebig University Giessen; 35392 Giessen Germany
| | - Simon M. Berkowicz
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
- Arid Ecosystems Research Center; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Rainer Horn
- Institute of Plant Nutrition and Soil Science; Christian Albrechts University of Kiel; 24118 Kiel Germany
| | - Martin Hagemann
- Institut für Biowissenschaften; Universität Rostock; D-18059 Rostock Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
- Arid Ecosystems Research Center; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
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