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Li Y, Sun X, Yang R, Guo L, Li C, Wang X, Li B, Liu H, Wang Q, Soleimani M, Ren Y, Sun W. Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6192-6203. [PMID: 38551467 DOI: 10.1021/acs.est.3c09460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Biological nitrogen fixation (BNF) has important ecological significance in mine tailing by contributing to the initial accumulation of nitrogen. In addition to chemolithotrophic and heterotrophic BNF, light may also fuel BNF in oligotrophic mine tailings. However, knowledge regarding the occurrence and ecological significance of this biogeochemical process in mine tailings remains ambiguous. The current study observed phototrophic BNF in enrichment cultures established from three primary successional stages (i.e., original tailings, biological crusts, and pioneer plants) of tailings. Notably, phototrophic BNF in tailings may be more active at vegetation stages (i.e., biological crusts and pioneering plants) than in bare tailings. DNA-stable isotope probing identified Roseomonas species as potential aerobic anoxygenic phototrophs responsible for phototrophic BNF. Furthermore, metagenomic binning as well as genome mining revealed that Roseomonas spp. contained essential genes involved in nitrogen fixation, anoxygenic photosynthesis, and carbon fixation, suggesting their genetic potential to mediate phototrophic BNF. A causal inference framework equipped with the structural causal model suggested that the enrichment of putative phototrophic diazotrophic Roseomonas may contribute to an elevated total nitrogen content during primary succession in these mine tailings. Collectively, our findings suggest that phototrophic diazotrophs may play important roles in nutrient accumulation and hold the potential to facilitate ecological succession in tailings.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Cangbai Li
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Huaqing Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Youhua Ren
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Jech SD, Day N, Barger NN, Antoninka A, Bowker MA, Reed S, Tucker C. Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration. Microorganisms 2023; 11:2570. [PMID: 37894228 PMCID: PMC10608944 DOI: 10.3390/microorganisms11102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.
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Affiliation(s)
- Sierra D Jech
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Natalie Day
- Colorado Water Science Center, U.S. Geological Survey, Grand Junction, CO 81506, USA
| | - Nichole N Barger
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Anita Antoninka
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86001, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86001, USA
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86001, USA
| | - Sasha Reed
- Southwest Biological Science Center, U.S. Geological Survey, Moab, UT 84532, USA
| | - Colin Tucker
- Manti-La Sal National Forest, U.S. Forest Service, Monticello, UT 84535, USA
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Yadav P, Singh RP, Hashem A, Abd_Allah EF, Santoyo G, Kumar A, Gupta RK. Enhancing Biocrust Development and Plant Growth through Inoculation of Desiccation-Tolerant Cyanobacteria in Different Textured Soils. Microorganisms 2023; 11:2507. [PMID: 37894165 PMCID: PMC10609203 DOI: 10.3390/microorganisms11102507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/17/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
In recent years, there has been a burgeoning interest in the utilization of cyanobacteria for the purpose of land rehabilitation via enhancements in soil fertility, prevent erosion, and counter desertification. This study evaluated the ability of Nostoc calcicola BOT1, Scytonema sp. BOT2, and their consortia to form biocrusts on the substrate of coarse sand, fine sand, and loamy soil. A nutrient- and water-deficient substrate was inoculated with cyanobacteria to facilitate biocrust formation and evaluate their impact on agriculture. Cyanobacteria inoculation resulted in significant improvements in soil fertility, especially in coarse and fine sand, which initially had the lowest fertility. The findings of this investigation underscore that the consortium of cyanobacteria exhibited greater efficacy than individual strains in enhancing soil fertility and stimulating plant growth. The loamy soil treated with the consortium had the highest plant growth across all soil types, in contrast to the individual strains. The consortium of cyanobacteria showed promising results in promoting biocrust formation and fostering rice seedling growth in fine sand. This study provides empirical evidence supporting the potential utility of cyanobacterial consortia as a valuable tool for the rehabilitation of degraded land. Furthermore, the results indicate that cyanobacterial species can persist in soil environments even following prolonged periods of desiccation.
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Affiliation(s)
- Priya Yadav
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (P.Y.); (R.P.S.)
| | - Rahul Prasad Singh
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (P.Y.); (R.P.S.)
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (A.H.)
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia; (E.F.A.)
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico; (G.S.)
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | - Rajan Kumar Gupta
- Laboratory of Algal Research, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India; (P.Y.); (R.P.S.)
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Gabay T, Rotem G, Gillor O, Ziv Y. Understanding changes in biocrust communities following phosphate mining in the Negev Desert. ENVIRONMENTAL RESEARCH 2022; 207:112200. [PMID: 34688640 DOI: 10.1016/j.envres.2021.112200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/15/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Biocrusts are key ecosystem engineers that are being destroyed due to anthropogenic disturbances such as trampling, agriculture and mining. In hyper-arid regions of the Negev Desert, phosphate has been mined for over six decades, altering the natural landscape over large spatial scales. In recent years, restoration-oriented practices were mandated in mining sites, however, the impact of such practices on the ecosystem, particularly the biocrust layer, has not been tested. Here, we evaluated post-mining biocrust bacterial communities and compared them to undisturbed (reference) biocrusts. We collected samples from four mining sites (each restored at a different year) and their corresponding reference sites. We hypothesized that post-mining bacterial communities would differ significantly from reference communities, given the slow regeneration of the biocrust. We also hypothesized that bacterial communities would vary among post-mining plots based on their restoration age. To test these hypotheses, we assessed the abundance and diversity of bacterial communities by sequencing the 16S rDNA and their photosynthetic potential by quantifying the abundance of cyanobacteria and chlorophyll a. The bacterial diversity was lower, and community composition differed significantly between post-mining and reference biocrusts. In addition, cyanobacteria abundances and chlorophyll a content were lower in post-mining biocrusts, indicating lower photosynthetic potential. However, no significant changes in bacterial communities were detected, regardless of the restoration age. We suggest that the practices implemented in the Negev mines may not support the recovery of the biocrust bacterial communities, particularly the cyanobacteria. Thus, active restoration measures are needed to accelerate the regeneration time of biocrusts at the hyper-arid Negev mines.
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Affiliation(s)
- Talia Gabay
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Israel; Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Israel
| | - Guy Rotem
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Israel
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Israel.
| | - Yaron Ziv
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501, Israel.
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Moreira C Fernandes V, Giraldo-Silva A, Roush D, Garcia-Pichel F. Coleofasciculaceae, a Monophyletic Home for the Microcoleus steenstrupii Complex and Other Desiccation-tolerant Filamentous Cyanobacteria. JOURNAL OF PHYCOLOGY 2021; 57:1563-1579. [PMID: 34289106 DOI: 10.1111/jpy.13199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/09/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria classified as Microcoleus steenstrupii play a significant role as pioneers of biological soil crusts (biocrusts), but this taxon is recognized to constitute a diverse complex of strains and field populations. With the aim of clarifying its systematics, we conducted a polyphasic characterization of this and allied taxa. A 16S ribosomal gene meta-analysis of published environmental sequences showed that the complex encompasses a variety of well supported genus-level clades with clade-specific environmental preferences, indicating significant niche differentiation. Fifteen strains in the M. steenstrupii complex were selected as representative of naturally occurring clades and studied using 16S rRNA gene phylogeny, morphology, and niche delineation with respect to temperature and rainfall. Bayesian phylogenetic reconstructions within a comprehensive, curated database of long 16S rRNA cyanobacterial sequences (1,000 base pairs or more) showed that they all belonged in a monophyletic, family-level clade (91.4% similarity) that included some other known genera of desiccation-resistant, largely terrestrial, filamentous, nonheterocystous cyanobacteria, including Coleofasciculus, the type genus for the family Coleofasciculaceae. To accommodate this biodiversity, we redescribe the Coleofasciculaceae, now composed of 11 genera, among which six are newly described herein (Funiculus, Parifilum, Arizonema, Crassifilum, Crustifilum, and Allocoleopsis), and five were previously recognized (Porphyrosiphon, Coleofasciculus, Pycnacronema, Potamolinea, and Wilmottia). We provide an evaluation of their respective niches and global distributions within biocrusts based on published molecular data. This new systematics treatment should help simplify and improve our understanding of the biology of terrestrial cyanobacteria.
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Affiliation(s)
- Vanessa Moreira C Fernandes
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, USA
| | - Ana Giraldo-Silva
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, USA
| | - Daniel Roush
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, USA
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, USA
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Beneficial cyanosphere heterotrophs accelerate establishment of cyanobacterial biocrust. Appl Environ Microbiol 2021; 87:e0123621. [PMID: 34379492 DOI: 10.1128/aem.01236-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological soil crusts (biocrusts) are communities of microbes that inhabit the surface of arid soils and provide essential services to dryland ecosystems. While resistant to extreme environmental conditions, biocrusts are susceptible to anthropogenic disturbances that can deprive ecosystems of these valuable services for decades. Until recently, culture-based efforts to produce inoculum for cyanobacterial biocrust restoration in the Southwestern US focused on producing and inoculating the most abundant primary producers and biocrust pioneers, Microcoleus vaginatus and members of the family Coleofasciculaceae (aka "Microcoleus streenstrupii complex"). The discovery that a unique microbial community characterized by diazotrophs is intimately associated with M. vaginatus, known as the "cyanosphere", suggests a symbiotic division of labor in which nutrients are traded between phototrophs and heterotrophs. To probe the potential use of such cyanosphere members in the restoration of biocrusts, we performed co-inoculations of soil substrates with cyanosphere constituents. This resulted in more rapid cyanobacterial growth over inoculations with the cyanobacterium alone. Additionally, we found that the mere addition of beneficial heterotrophs enhanced the formation of a cohesive biocrust without the need of additional phototrophic biomass within native soils that contain trace amounts of biocrust cyanobacteria. Our findings support the hitherto unknown role of beneficial heterotrophic bacteria in the establishment and growth of biocrusts and allow us to make recommendations concerning biocrust restoration efforts based on the presence of remnant biocrust communities in disturbed areas. Future biocrust restoration efforts should consider cyanobacteria and their beneficial heterotrophic community as inoculants. Importance The advancement of biocrust restoration methodologies for cyanobacterial biocrusts has been largely achieved through trial and error. Successes and failures could not always be traced back to particular factors. The investigation and application of foundational microbial interactions existing within biocrust communities is a crucial step toward informed and repeatable biocrust restoration methodologies.
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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: 17] [Impact Index Per Article: 5.7] [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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A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus. ISME JOURNAL 2020; 15:282-292. [PMID: 32968213 DOI: 10.1038/s41396-020-00781-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/26/2020] [Accepted: 09/10/2020] [Indexed: 02/01/2023]
Abstract
Microcoleus vaginatus plays a prominent role as both primary producer and pioneer in biocrust communities from dryland soils. And yet, it cannot fix dinitrogen, essential in often nitrogen-limited drylands. But a diazotroph-rich "cyanosphere" has been described in M. vaginatus, hinting that there exists a C for N exchange between the photoautotroph and heterotrophic diazotrophs. We provide evidence for this by establishing such a symbiosis in culture and by showing that it is selective and dependent on nitrogen availability. In natural populations, provision of nitrogen resulted in loss of diazotrophs from the cyanosphere of M. vaginatus compared to controls, but provision of phosphorus did not. Co-culturing of pedigreed cyanosphere diazotroph isolates with axenic M. vaginatus resulted in copious growth in C and N-free medium, but co-culture with non-cyanosphere diazotrophs or other heterotrophs did not. Unexpectedly, bundle formation in M. vaginatus, diacritical to the genus but not seen in axenic culture, was restored in vitro by imposed nitrogen limitation or, even more strongly, by co-culture with diazotrophic partners, implicating this trait in the symbiosis. Our findings provide direct evidence for a symbiotic relationship between M. vaginatus and its cyanosphere and help explain how it can be a global pioneer in spite of its genetic shortcomings.
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Antoninka A, Faist A, Rodriguez‐Caballero E, Young KE, Chaudhary VB, Condon LA, Pyke DA. Biological soil crusts in ecological restoration: emerging research and perspectives. Restor Ecol 2020. [DOI: 10.1111/rec.13201] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Anita Antoninka
- School of Forestry Northern Arizona University 200 E Pine Knoll Drive, Flagstaff AZ 86011 U.S.A
| | - Akasha Faist
- Department of Animal and Range Sciences New Mexico State University Box 30003 MSC 3‐I, Las Cruces NM 88003 U.S.A
| | - Emilio Rodriguez‐Caballero
- Centro de Investigación de Colecciones Científicas de la Universidad de Almería (CECOUAL) University of Almería 04120 Almería Spain
| | - Kristina E. Young
- Department of Biological Sciences University of Texas at El Paso 500 West University Avenue, El Paso TX 79968 U.S.A
| | - V. Bala Chaudhary
- Department of Environmental Science and Studies DePaul University 1110 West Belden Avenue, Chicago IL 60614 U.S.A
| | - Lea A. Condon
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR 97331 U.S.A
| | - David A. Pyke
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR 97331 U.S.A
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A Fog-Irrigated Soil Substrate System Unifies and Optimizes Cyanobacterial Biocrust Inoculum Production. Appl Environ Microbiol 2020; 86:AEM.00624-20. [PMID: 32358005 DOI: 10.1128/aem.00624-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/23/2020] [Indexed: 02/01/2023] Open
Abstract
Biological soil crusts (biocrusts) are globally important microbial communities inhabiting the top layer of soils. They provide multiple services to dryland ecosystems but are particularly vulnerable to anthropogenic disturbance from which they naturally recover only slowly. Assisted inoculation with cyanobacteria is held as a promising approach to promote biocrust regeneration. Two different methodologies have been developed for this purpose: mass cultivation of biocrust pioneer species (such as the cyanobacteria Microcoleus spp.) on cellulose supports, and polymicrobial cultivation of biocrusts in soils within greenhouse settings. Here, we aimed to test a novel method to grow cyanobacterial biocrust inoculum based on fog irrigation of soil substrates (FISS) that can be used with either culture-based or mixed-community approaches. We found that the FISS system presents clear advantages over previous inoculum production methodologies; overall, FISS eliminates the need for specialized facilities and decreases user effort. Specifically, there were increased microbial yields and simplification of design compared to those of the culture-based and mixed-community approaches, respectively. Its testing also allows us to make recommendations on underexplored aspects of biocrust restoration: (i) field inoculation levels should be equal to or greater than the biomass found in the substrate and (ii) practices regarding evaluation of cyanobacterial biomass should, under certain circumstances, include proxies additional to chlorophyll a IMPORTANCE Biocrust inoculum production for use in dryland rehabilitation is a powerful tool in combating the degradation of dryland ecosystems. However, the facilities and effort required to produce high-quality inoculum are often a barrier to effective large-scale implementation by land managers. By unifying and optimizing the two foremost methods for cyanobacterial biocrust inoculum production, our work improves on the ease and cost with which biocrust restoration technology can be translated to practical widespread implementation.
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11
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Giraldo-Silva A, Fernandes VMC, Bethany J, Garcia-Pichel F. Niche Partitioning with Temperature among Heterocystous Cyanobacteria ( Scytonema spp., Nostoc spp., and Tolypothrix spp.) from Biological Soil Crusts. Microorganisms 2020; 8:microorganisms8030396. [PMID: 32178304 PMCID: PMC7142793 DOI: 10.3390/microorganisms8030396] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 11/16/2022] Open
Abstract
Heterocystous cyanobacteria of biocrusts are key players for biological fixation in drylands, where nitrogen is only second to water as a limiting resource. We studied the niche partitioning among the three most common biocrust heterocystous cyanobacteria sts using enrichment cultivation and the determination of growth responses to temperature in 30 representative isolates. Isolates of Scytonema spp. were most thermotolerant, typically growing up to 40 °C, whereas only those of Tolypothrix spp. grew at 4 °C. Nostoc spp. strains responded well at intermediate temperatures. We could trace the heat sensitivity in Nostoc spp. and Tolypothrix spp. to N2-fixation itself, because the upper temperature for growth increased under nitrogen replete conditions. This may involve an inability to develop heterocysts (specialized N2-fixing cells) at high temperatures. We then used a meta-analysis of biocrust molecular surveys spanning four continents to test the relevance of this apparent niche partitioning in nature. Indeed, the geographic distribution of the three types was clearly constrained by the mean local temperature, particularly during the growth season. This allows us to predict a potential shift in dominance in many locales as a result of global warming, to the benefit of Scytonema spp. populations.
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Affiliation(s)
- Ana Giraldo-Silva
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.G.-S.); (J.B.)
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesing Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Vanessa M. C. Fernandes
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.G.-S.); (J.B.)
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesing Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Julie Bethany
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.G.-S.); (J.B.)
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesing Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; (A.G.-S.); (J.B.)
- Center for Fundamental and Applied Microbiomics (CFAM), Biodesing Institute, Arizona State University, Tempe, AZ 85287, USA
- Correspondence: , Tel.: +1-4807270498
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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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Faist AM, Antoninka AJ, Belnap J, Bowker MA, Duniway MC, Garcia‐Pichel F, Nelson C, Reed SC, Giraldo‐Silva A, Velasco‐Ayuso S, Barger NN. Inoculation and habitat amelioration efforts in biological soil crust recovery vary by desert and soil texture. Restor Ecol 2020. [DOI: 10.1111/rec.13087] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Akasha M. Faist
- Department of Animal and Range SciencesNew Mexico State University Las Cruces NM 88003 U.S.A
| | | | - Jayne Belnap
- Southwest Biological Science CenterU.S. Geological Survey Moab UT 84532 U.S.A
| | - Matthew A. Bowker
- School of ForestryNorthern Arizona University Flagstaff AZ 86011 U.S.A
| | - Michael C. Duniway
- Southwest Biological Science CenterU.S. Geological Survey Moab UT 84532 U.S.A
| | - Ferran Garcia‐Pichel
- School of Life Sciences and Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State University Tempe AZ 85281 U.S.A
| | - Corey Nelson
- School of Life Sciences and Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State University Tempe AZ 85281 U.S.A
| | - Sasha C. Reed
- Southwest Biological Science CenterU.S. Geological Survey Moab UT 84532 U.S.A
| | - Ana Giraldo‐Silva
- School of Life Sciences and Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State University Tempe AZ 85281 U.S.A
| | - Sergio Velasco‐Ayuso
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de AgronomíaUniversidad de Buenos Aires, Ciudad Autónoma de Buenos Aires Buenos Aires C1417DSE Argentina
| | - Nichole N. Barger
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO 80309 U.S.A
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Szyja M, Menezes AGDS, Oliveira FDA, Leal I, Tabarelli M, Büdel B, Wirth R. Neglected but Potent Dry Forest Players: Ecological Role and Ecosystem Service Provision of Biological Soil Crusts in the Human-Modified Caatinga. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Machado-de-Lima NM, Fernandes VMC, Roush D, Velasco Ayuso S, Rigonato J, Garcia-Pichel F, Branco LHZ. The Compositionally Distinct Cyanobacterial Biocrusts From Brazilian Savanna and Their Environmental Drivers of Community Diversity. Front Microbiol 2019; 10:2798. [PMID: 31921007 PMCID: PMC6929519 DOI: 10.3389/fmicb.2019.02798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/18/2019] [Indexed: 02/01/2023] Open
Abstract
The last decade was marked by efforts to define and identify the main cyanobacterial players in biological crusts around the world. However, not much is known about biocrusts in Brazil’s tropical savanna (cerrado), despite the existence of environments favorable to their development and ecological relevance. We examined the community composition of cyanobacteria in biocrusts from six sites distributed in the Southeast of the country using high throughput sequencing of 16S rRNA and phylogenetic placement in the wider context of biocrusts from deserts. Sequences ascribable to 22 genera of cyanobacteria were identified. Although a significant proportion of sequences did not match those of known cyanobacteria, several clades of Leptolyngbya and Porphyrosiphon were found to be the most abundant. We identified significant differences in dominance and overall composition among the cerrado sites, much larger than within-site variability. The composition of cerrado cyanobacterial communities was distinct from those known in biocrusts from North American deserts. Among several environmental drivers considered, the opposing trend of annual precipitation and mean annual temperature best explained the variability in community composition within Brazilian biocrusts. Their compositional uniqueness speaks of the need for dedicated efforts to study the ecophysiology of tropical savanna biocrust and their roles in ecosystem function for management and preservation.
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Affiliation(s)
- Náthali Maria Machado-de-Lima
- Microbiology Graduation Program, Department of Zoology and Botany, São Paulo State University (UNESP), São Paulo, Brazil
| | | | - Daniel Roush
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Sergio Velasco Ayuso
- Facultad de Agronomía, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Janaina Rigonato
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Piracicaba, Brazil
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Luis Henrique Zanini Branco
- Microbiology Graduation Program, Department of Zoology and Botany, São Paulo State University (UNESP), São Paulo, Brazil
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Fick SE, Day N, Duniway MC, Hoy‐Skubik S, Barger NN. Microsite enhancements for soil stabilization and rapid biocrust colonization in degraded drylands. Restor Ecol 2019. [DOI: 10.1111/rec.13071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephen E. Fick
- US Geological Survey Southwest Biological Science Center Moab UT U.S.A
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO U.S.A
| | - Natalie Day
- US Geological Survey Southwest Biological Science Center Moab UT U.S.A
| | | | - Sean Hoy‐Skubik
- US Geological Survey Southwest Biological Science Center Moab UT U.S.A
| | - Nichole N. Barger
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO U.S.A
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Pietrasiak N, Osorio-Santos K, Shalygin S, Martin MP, Johansen JR. When Is A Lineage A Species? A Case Study In Myxacorys gen. nov. (Synechococcales: Cyanobacteria) With The Description of Two New Species From The Americas. JOURNAL OF PHYCOLOGY 2019; 55:976-996. [PMID: 31233617 DOI: 10.1111/jpy.12897] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Soil cyanobacteria are crucial components of biological soil crusts and carry out many functions in dryland ecosystems. Despite this importance, their taxonomy and population genetics remain poorly known. We isolated 42 strains of simple filamentous cyanobacteria previously identified as Pseudophormidium hollerbachianum from 26 desert locations in the North and South America and characterized these strains using a total evidence approach, that is, using both morphological and molecular data to arrive at taxonomic decisions. Based on a phylogenetic analysis of 16S rRNA gene sequences, we propose and characterize Myxacorys gen. nov. with two new species Myxacorys chilensis, the generitype, and M. californica. We also found distinct 16S-23S ITS sequence variability within species in our dataset. Especially interesting was the presence of two distinct lineages of M. californica obtained from locations in close spatial proximity (within a few meters to kilometers from each other) suggesting niche differentiation. The detection of such unrecognized lineage-level variability in soil cyanobacteria has important implications for biocrust restoration practices and conservation efforts.
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Affiliation(s)
- Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, 945 College Drive., Las Cruces, New Mexico, 88003, USA
| | - Karina Osorio-Santos
- Department of Comparative Biology, Faculty of Science, Universidad Nacional Autonóma de México, Coyoacán, Distrito Federal, 04510, México
| | - Sergei Shalygin
- Plant and Environmental Sciences Department, New Mexico State University, 945 College Drive., Las Cruces, New Mexico, 88003, USA
| | - Michael P Martin
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Sciences, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
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Optimizing the Production of Nursery-Based Biological Soil Crusts for Restoration of Arid Land Soils. Appl Environ Microbiol 2019; 85:AEM.00735-19. [PMID: 31152015 PMCID: PMC6643228 DOI: 10.1128/aem.00735-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Biocrust communities provide important ecosystem services for arid land soils, such as soil surface stabilization promoting erosion resistance and contributing to overall soil fertility. Anthropogenic degradation to biocrust communities (through livestock grazing, agriculture, urban sprawl, and trampling) is common and significant, resulting in a loss of those ecosystem services. Losses impact both the health of the native ecosystem and the public health of local populations due to enhanced dust emissions. Because of this, approaches for biocrust restoration are being developed worldwide. Here, we present optimization of a nursery-based approach to scaling up the production of biocrust inoculum for field restoration with respect to temporal dynamics and reuse of biological materials. Unexpectedly, we also report on complex population dynamics, significant spatial variability, and lower than expected yields that we ascribe to the demonstrable presence of cyanobacterial pathogens, the spread of which may be enhanced by some of the nursery production standard practices. Biological soil crusts (biocrusts) are topsoil communities formed by cyanobacteria or other microbial primary producers and are typical of arid and semiarid environments. Biocrusts promote a range of ecosystem services, such as erosion resistance and soil fertility, but their degradation by often anthropogenic disturbance brings about the loss of these services. This has prompted interest in developing restoration techniques. One approach is to source biocrust remnants from the area of interest for scale-up cultivation in a microbial “nursery” that produces large quantities of high-quality inoculum for field deployment. However, growth dynamics and the ability to reuse the produced inoculum for continued production have not been assessed. To optimize production, we followed nursery growth dynamics of biocrusts from cold (Great Basin) and hot (Chihuahuan) deserts. Peak phototrophic biomass was attained between 3 and 7 weeks in cold desert biocrusts and at 12 weeks in those from hot deserts. We also reused the resultant biocrust inoculum to seed successive incubations, tracking both phototroph biomass and cyanobacterial community structure using 16S rRNA gene amplicon sequencing. Hot desert biocrusts showed little to no viability upon reinoculation, while cold desert biocrusts continued to grow, but at the expense of progressive shifts in species composition. This leads us to discourage the reuse of nursery-grown inoculum. Surprisingly, growth was highly variable among replicates, and overall yields were low, a fact that we attribute to the demonstrable presence of virulent and stochastically distributed but hitherto unknown cyanobacterial pathogens. We provide recommendations to avoid pathogen incidence in the process. IMPORTANCE Biocrust communities provide important ecosystem services for arid land soils, such as soil surface stabilization promoting erosion resistance and contributing to overall soil fertility. Anthropogenic degradation to biocrust communities (through livestock grazing, agriculture, urban sprawl, and trampling) is common and significant, resulting in a loss of those ecosystem services. Losses impact both the health of the native ecosystem and the public health of local populations due to enhanced dust emissions. Because of this, approaches for biocrust restoration are being developed worldwide. Here, we present optimization of a nursery-based approach to scaling up the production of biocrust inoculum for field restoration with respect to temporal dynamics and reuse of biological materials. Unexpectedly, we also report on complex population dynamics, significant spatial variability, and lower than expected yields that we ascribe to the demonstrable presence of cyanobacterial pathogens, the spread of which may be enhanced by some of the nursery production standard practices.
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19
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Spectral Response Analysis: An Indirect and Non-Destructive Methodology for the Chlorophyll Quantification of Biocrusts. REMOTE SENSING 2019. [DOI: 10.3390/rs11111350] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chlorophyll a concentration (Chla) is a well-proven proxy of biocrust development, photosynthetic organisms’ status, and recovery monitoring after environmental disturbances. However, laboratory methods for the analysis of chlorophyll require destructive sampling and are expensive and time consuming. Indirect estimation of chlorophyll a by means of soil surface reflectance analysis has been demonstrated to be an accurate, cheap, and quick alternative for chlorophyll retrieval information, especially in plants. However, its application to biocrusts has yet to be harnessed. In this study we evaluated the potential of soil surface reflectance measurements for non-destructive Chla quantification over a range of biocrust types and soils. Our results revealed that from the different spectral transformation methods and techniques, the first derivative of the reflectance and the continuum removal were the most accurate for Chla retrieval. Normalized difference values in the red-edge region and common broadband indexes (e.g., normalized difference vegetation index (NDVI)) were also sensitive to changes in Chla. However, such approaches should be carefully adapted to each specific biocrust type. On the other hand, the combination of spectral measurements with non-linear random forest (RF) models provided very good fits (R2 > 0.94) with a mean root mean square error (RMSE) of about 6.5 µg/g soil, and alleviated the need for a specific calibration for each crust type, opening a wide range of opportunities to advance our knowledge of biocrust responses to ongoing global change and degradation processes from anthropogenic disturbance.
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Couradeau E, Giraldo-Silva A, De Martini F, Garcia-Pichel F. Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere. MICROBIOME 2019; 7:55. [PMID: 30944036 PMCID: PMC6448292 DOI: 10.1186/s40168-019-0661-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/11/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentous, non-nitrogen-fixing cyanobacterium Microcoleus vaginatus is a pioneer primary producer, often the dominant member of the biocrust microbiome, and the main source of leaked organic carbon. We hypothesized that, by analogy to the rhizosphere of plant roots, M. vaginatus may shape the microbial populations of heterotrophs around it, forming a specialized cyanosphere. RESULTS By physically isolating bundles of M. vaginatus from biocrusts, we were able to study the composition of the microbial populations attached to it, in comparison to the bulk soil crust microbiome by means of high-throughput 16S rRNA sequencing. We did this in two M. vaginatus-dominated biocrust from distinct desert biomes. We found that a small, selected subset of OTUs was significantly enriched in close proximity to M. vaginatus. Furthermore, we also found that a majority of bacteria (corresponding to some two thirds of the reads) were significantly more abundant away from this cyanobacterium. Phylogenetic placements suggest that all typical members of the cyanosphere were copiotrophs and that many were diazotrophs (Additional file 1: Tables S2 and S3). Nitrogen fixation genes were in fact orders of magnitude more abundant in this cyanosphere than in the bulk biocrust soil as assessed by qPCR. By contrary, competition for light, CO2, and low organic carbon concentrations defined at least a part of the OTUs segregating from the cyanobacterium. CONCLUSIONS We showed that M. vaginatus acts as a significant spatial organizer of the biocrust microbiome. On the one hand, it possesses a compositionally differentiated cyanosphere that concentrates the nitrogen-fixing function. We propose that a mutualism based on C for N exchange between M. vaginatus and copiotrophic diazotrophs helps sustains this cyanosphere and that this consortium constitutes the true pioneer community enabling the colonization of nitrogen-poor soils. On the other hand, a large number of biocrust community members segregate away from the vicinity of M. vaginatus, potentially through competition for light or CO2, or because of a preference for oligotrophy.
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Affiliation(s)
- Estelle Couradeau
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85287 USA
- Laboratoire Biogéosciences, Université de Bourgogne, Dijon, France
- Present Address: Joint Genome Institute (DOE), Lawrence Berkeley National Lab (LBNL), 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ana Giraldo-Silva
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85287 USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85282 USA
| | - Francesca De Martini
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85287 USA
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85287 USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85282 USA
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Roncero-Ramos B, Muñoz-Martín MÁ, Chamizo S, Fernández-Valbuena L, Mendoza D, Perona E, Cantón Y, Mateo P. Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe. PeerJ 2019; 7:e6169. [PMID: 30627491 PMCID: PMC6321753 DOI: 10.7717/peerj.6169] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/27/2018] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
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Affiliation(s)
| | | | - Sonia Chamizo
- Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy
| | | | - Diego Mendoza
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elvira Perona
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Yolanda Cantón
- Departamento de Agronomía, Universidad de Almería, Almería, Spain.,Centro de Investigación de Colecciones Científicas de la Universidad de Almería, Universidad de Almería, Almería, Spain
| | - Pilar Mateo
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
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Costa OYA, Raaijmakers JM, Kuramae EE. Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation. Front Microbiol 2018; 9:1636. [PMID: 30083145 PMCID: PMC6064872 DOI: 10.3389/fmicb.2018.01636] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/30/2018] [Indexed: 11/15/2022] Open
Abstract
A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins, and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment, and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling, and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial EPSs and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health, and fertility.
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Affiliation(s)
- Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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Next-Generation Sequencing Library Preparation for 16S rRNA Microbiome Analysis After Serpin Treatment. Methods Mol Biol 2018; 1826:213-221. [PMID: 30194603 DOI: 10.1007/978-1-4939-8645-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Serine protease inhibitors, serpins, can have profound effects on many systems in the body including immune defense systems. The microbiome, specifically the gut and lung bacterial microbiota, is now known, under some conditions, to alter immune defenses. DNA library preparation for microbiome studies is a procedure that prepares microbial genomic DNA to be sequenced in next-generation sequencing platforms. The construction involves a PCR reaction that will amplify the 16S rRNA gene and will incorporate a specific index and adaptors to the fragments. After confirmation of the product amplification by gel electrophoresis, samples will be later normalized to the same DNA amount of 240 ng. Final concentration of the library is validated by quantitative PCR (qPCR).Here we describe methods to analyze changes in the microbiome after treatment with immune-modulating agents, specifically serpins.
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