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Giraldo-Silva A, Masiello CA. Environmental conditions play a key role in controlling the composition and diversity of Colombian biocrust microbiomes. Front Microbiol 2024; 15:1236554. [PMID: 38725684 PMCID: PMC11081033 DOI: 10.3389/fmicb.2024.1236554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 03/11/2024] [Indexed: 05/12/2024] Open
Abstract
Drylands soils worldwide are naturally colonized by microbial communities known as biocrusts. These soil microbiomes render important ecosystem services associated with soil fertility, water holding capacity, and stability to the areas they cover. Because of the importance of biocrusts in the global cycling of nutrients, there is a growing interest in describing the many microbial configurations these communities display worldwide. However, comprehensive 16S rRNA genes surveys of biocrust communities do not exist for much of the planet: for example, in the continents of South America and the northern part of Africa. The absence of a global understanding of biocrust biodiversity has lead us to assign a general importance to community members that may, in fact, be regional. Here we report for the first time the presence of biocrusts in Colombia (South America) through 16S rRNA genes surveys across an arid, a semi-arid and a dry subtropical region within the country. Our results constitute the first glance of the Bacterial/Archaeal communities associated with South American biocrust microbiomes. Communities where cyanobacteria other than Microcoleus vaginatus prevail, despite the latter being considered a key species elsewhere, illustrate differentiable results in these surveys. We also find that the coastal biocrust communities in Colombia include halo-tolerant and halophilic species, and that niche preference of some nitrogen fixing organisms deviate from previously described global trends. In addition, we identified a high proportion (ranging from 5 to 70%, in average) of cyanobacterial sequences that did not match any formally described cyanobacterial species. Our investigation of Colombian biocrusts points to highly diverse communities with climatic regions controlling taxonomic configurations. They also highlight an extensive local diversity to be discovered which is central to better design management and restoration strategies for drylands soils currently undergoing disturbances due to land use and global warming. Finally, this field study highlights the need for an improved mechanistic understanding of the response of key biocrust community members to changes in moisture and temperature.
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Affiliation(s)
- Ana Giraldo-Silva
- Department of Science, Ecology Group and Institute for Multidisciplinary Research in Applied Biology, Public University of Navarre (UPNA), Pamplona, Spain
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
| | - Caroline A. Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
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2
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Zhou X, Liang B, Zhang T, Xiong Q, Ma X, Chen L. Co-inoculation of fungi and desert cyanobacteria facilitates biological soil crust formation and soil fertility. Front Microbiol 2024; 15:1377732. [PMID: 38650889 PMCID: PMC11033444 DOI: 10.3389/fmicb.2024.1377732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
The inoculation of cyanobacteria for enriching soil nutrients and forming biological soil crusts (BSCs) is considered an effective means to restore degraded soil. However, there are limited studies on the application of co-inoculation of fungi and cyanobacteria for degraded soil remediation. In this study, a high exopolysaccharide-secreting fungi Zh2 was isolated from lichen BSCs in Hobq Desert, and co-inoculated with a cyanobacterial strain identified as Phormidium tenue in different proportions to form BSCs on sand during a 35 days incubation period. Results revealed significant differences in crust biomass and soil properties among crusts with different cyanobacterial/fungal inoculation ratios. Microbial biomass, soil nutrient content and enzyme activities in crusts co-inoculated with cyanobacteria and fungi were higher than those inoculated with cyanobacteria and fungi alone. The inoculation of cyanobacteria contributed to the fulvic-like accumulation, and the inoculated fungi significantly increased the humic-like content and soil humification. Redundancy analysis showed that the inoculation of cyanobacteria was positively correlated with the activities of urease and phosphatase, and the content of fulvic-like. Meanwhile, the inoculation of fungi was positively correlated with the contents of total carbon, total nitrogen and humic-like, the activities of catalase and sucrase. Cyanobacteria and fungi play distinct roles in improving soil fertility and accumulating dissolved organic matter. This study provides new insights into the effects of cyanobacteria and fungi inoculations on the formation and development of cyanobacterial-fungus complex crusts, offering a novel method for accelerating induced crust formation on the surface of sand.
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Affiliation(s)
- Xiangjun Zhou
- Huangshi Key Laboratory of Prevention and Control of Soil Pollution, College of Urban and Environmental Sciences, Hubei Normal University, Huangshi, China
- Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, School of Resource and Environmental Sciences, Wuhan University, Wuhan, China
| | - Bin Liang
- Huangshi Key Laboratory of Prevention and Control of Soil Pollution, College of Urban and Environmental Sciences, Hubei Normal University, Huangshi, China
| | - Tian Zhang
- Huangshi Key Laboratory of Prevention and Control of Soil Pollution, College of Urban and Environmental Sciences, Hubei Normal University, Huangshi, China
| | - Qiao Xiong
- Huangshi Key Laboratory of Prevention and Control of Soil Pollution, College of Urban and Environmental Sciences, Hubei Normal University, Huangshi, China
| | - Xiao Ma
- Huangshi Key Laboratory of Prevention and Control of Soil Pollution, College of Urban and Environmental Sciences, Hubei Normal University, Huangshi, China
| | - Lanzhou Chen
- Hubei Key Laboratory of Biomass-Resources Chemistry and Environmental Biotechnology, School of Resource and Environmental Sciences, Wuhan University, Wuhan, China
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3
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Duan Y, Li Y, Zhao J, Zhang J, Luo C, Jia R, Liu X. Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China. MICROBIAL ECOLOGY 2024; 87:43. [PMID: 38363394 PMCID: PMC10873229 DOI: 10.1007/s00248-024-02359-2] [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: 11/15/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
Biological soil crusts (biocrusts) are considered "desert ecosystem engineers" because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties' improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China-lying at the highest latitude of any sandy land in the country-was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust-lichen-moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.
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Affiliation(s)
- Yulong Duan
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, 028300, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, 730000, China
| | - Yuqiang Li
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, 028300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, 730000, China
| | - Jianhua Zhao
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai, 200120, China
| | - Junbiao Zhang
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai, 200120, China
| | - Chun Luo
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai, 200120, China
| | - Rongliang Jia
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Zhongwei, 755007, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xinping Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, 028300, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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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: 1] [Impact Index Per Article: 0.5] [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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5
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Salazar-Hamm PS, Montoya KN, Montoya L, Cook K, Liphardt S, Taylor JW, Cook JA, Natvig DO. Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:996574. [PMID: 37746221 PMCID: PMC10512277 DOI: 10.3389/ffunb.2022.996574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/24/2022] [Indexed: 09/26/2023]
Abstract
Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.
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Affiliation(s)
| | - Kyana N. Montoya
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Kel Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Schuyler Liphardt
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
| | - Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
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6
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Becktell MC, Tucker S, Ozsoy AZ, Connor M. Identification of fungi found on desiccated human remains in an arid outdoor environment. J Forensic Sci 2022; 67:2048-2054. [PMID: 35593446 DOI: 10.1111/1556-4029.15066] [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: 01/20/2022] [Revised: 04/08/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Three fungi not previously reported on desiccated human remains were identified on cadavers at the Forensic Investigation Research Station (FIRS) in Whitewater, Colorado. The location of the FIRS provides the unique opportunity to observe the stages of decomposition in a high desert environment. The two cadavers used in the study were in the late stages of decomposition (PMI of approximately 1520 and 1820 days) to the point of desiccation and had developed an extensive black crust on the skin that remained. Skin samples of the two cadavers were taken and plated onto potato dextrose agar to determine whether fungi were present on the desiccated tissues. Three different fungi consistently dominated cultures grown from numerous samples taken from each cadaver. Based on morphological observations, nuclear rDNA sequence data, and phylogenetic analyses, two fungi were identified to species (Aureobasidium melanogenum and Didymella glomerata) and one fungus was identified to the genus level (Alternaria). These results will contribute to the understanding of the role that fungi might play in late-stage decomposition and the extended postmortem period.
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Affiliation(s)
- Margot C Becktell
- Department of Biological Sciences Colorado Mesa University, Grand Junction, Colorado, USA
| | - Selina Tucker
- University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - A Zeynep Ozsoy
- Department of Biological Sciences Colorado Mesa University, Grand Junction, Colorado, USA
| | - Melissa Connor
- Department of Social and Behavioral Sciences, Forensic Investigation Research Station, Colorado Mesa University, Grand Junction, Colorado, USA
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7
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Merges D, Dal Grande F, Greve C, Otte J, Schmitt I. Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions. Environ Microbiol 2021; 23:6637-6650. [PMID: 34697892 DOI: 10.1111/1462-2920.15802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/01/2021] [Indexed: 11/28/2022]
Abstract
Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.
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Affiliation(s)
- Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
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8
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Ndinga-Muniania C, Mueller RC, Kuske CR, Porras-Alfaro A. Seasonal variation and potential roles of dark septate fungi in an arid grassland. Mycologia 2021; 113:1181-1198. [PMID: 34686124 DOI: 10.1080/00275514.2021.1965852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High temperatures and extended drought in temperate and tropical arid ecosystems promote the colonization of diverse microenvironments by dark septate fungi (DSF). These fungi contribute to soil nutrient cycling, soil stabilization, and plant survival, but the roles of individual DSF species, their distributions, and their community diversity are poorly understood. The objective of this study was to evaluate the distribution, seasonal variation, and potential roles of DSF on plant growth. We collected biocrust (lichen-, moss-, and cyanobacterium-dominated biocrusts) soils at different depths and rhizosphere soils from two grasses, Bromus tectorum and Pleuraphis jamesii, in an arid grassland near Moab, Utah, USA. Seasonal variation of DSF was evaluated using culture-based approaches and compared with fungal community profiles from next-generation sequencing (NGS). Culturing showed that DSF were 30% more abundant in biocrusts compared with the focal rhizospheres. The abundance of DSF varied seasonally in belowground samples (rhizosphere and below-biocrust), with a significant increase during the summer months. Pleosporales was the dominant order (35%) in both biocrust and rhizosphere soils out of 817 isolated fungi. Dominant DSF genera in culture included Alternaria, Preussia, Cladosporium, Phoma, and an unknown Pleosporales. Similar results were observed in biocrust and rhizosphere soils NGS. Further, seed germination experiments using dominant taxa were conducted to determine their potential roles on germination and seedling growth using maize as a model plant. Cladosporium and unknown Pleosporales isolates showed plant growth-promoting ability. The variation in abundance of DSF, their differential occurrence in different microenvironments, and their ability to grow in a xerotolerant medium reflect adaptations to summer environmental conditions and to changes in the abundance of organic matter, as well as a potential increase in plant investment in these fungi when heat and drought stresses are more severe.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, 55108, Minnesota
| | - Rebecca C Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Andrea Porras-Alfaro
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Division of Environmental Biology, National Science Foundation, Alexandria, Virginia 22314
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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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10
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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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11
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Canini F, Geml J, D'Acqui LP, Selbmann L, Onofri S, Ventura S, Zucconi L. Exchangeable cations and pH drive diversity and functionality of fungal communities in biological soil crusts from coastal sites of Victoria Land, Antarctica. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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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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Cao W, Xiong Y, Zhao D, Tan H, Qu J. Bryophytes and the symbiotic microorganisms, the pioneers of vegetation restoration in karst rocky desertification areas in southwestern China. Appl Microbiol Biotechnol 2020; 104:873-891. [PMID: 31822979 PMCID: PMC6943408 DOI: 10.1007/s00253-019-10235-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 01/03/2023]
Abstract
In karst rocky desertification areas, bryophytes coexist with algae, bacteria, and fungi on exposed calcareous rocks to form a bryophyte crust, which plays an irreplaceable role in the restoration of karst degraded ecosystems. We investigated the biodiversity of crust bryophytes in karst rocky desertification areas from Guizhou Province, China. A total of 145 species in 22 families and 56 genera were identified. According to frequency and coverage, seven candidate dominant mosses were screened out, and five drought-resistant indexes of them were measured. Hypnum leptothallum, Racopilum cuspidigerum, and Hyophila involuta have high drought adaptability. We explored the interactions between two dominant mosses (H. leptothallum, H. involuta) and the structure of microbial communities in three karst rocky desertification types. Microbial diversity and function analysis showed that both moss species and karst rocky desertification types affect microbial communities. Moss species much more strongly affected the diversity and changed the community composition of these microbial groups. Bacteria were more sensitive in the microbiome as their communities changed strongly between mosses and drought resistance factors. Moreover, several species of fungi and bacteria could be significantly associated with three drought-resistant indexes: Pro (free proline content), SOD (superoxide dismutase activity), and POD (peroxidase activity), which were closely related to the drought adaptability of mosses. Our results enforced the potential role of moss-associated microbes that are important components involved in the related biological processes when bryophytes adapted to arid habitats, or as one kind of promoters in the distribution pattern of early mosses succession in karst rocky desertification areas.
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Affiliation(s)
- Wei Cao
- College of Life Sciences, Guizhou University, Guiyang, 550025, China
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yuanxin Xiong
- College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Degang Zhao
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Hongying Tan
- Guiyang A'ha Lake National Wetland Park Management Division, Guiyang, 550002, China
| | - Jiaojiao Qu
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China.
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15
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Albright MBN, Mueller RC, Gallegos-Graves LV, Belnap J, Reed SC, Kuske CR. Interactions of Microhabitat and Time Control Grassland Bacterial and Fungal Composition. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00367] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Warren SD, Clair LL, Stark LR, Lewis LA, Pombubpa N, Kurbessoian T, Stajich JE, Aanderud ZT. Reproduction and Dispersal of Biological Soil Crust Organisms. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00344] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica. Microorganisms 2019; 7:microorganisms7070203. [PMID: 31323808 PMCID: PMC6681027 DOI: 10.3390/microorganisms7070203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/13/2019] [Accepted: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.
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Egidi E, Wood JL, Celestina C, May TW, Mele P, Edwards J, Powell J, Bissett A, Franks AE. Delving into the dark ecology: A continent-wide assessment of patterns of composition in soil fungal communities from Australian tussock grasslands. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Cultured Microfungal Communities in Biological Soil Crusts and Bare Soils at the Tabernas Desert, Spain. SOIL SYSTEMS 2019. [DOI: 10.3390/soilsystems3020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We examined the variations in microfungal communities from different surface types (cyanobacterial crusts, lichen-dominated crusts, and noncrusted bare surface) at two different positions—north-oriented slope and sun-exposed plain in the Tabernas Desert, Spain. A total of 77 species from 46 genera was isolated using the soil dilution plate method. The studied mycobiota, similar to the majority of desert mycobiotas, was dominated by melanin-containing species. However, in the Tabernas crusts, unlike the studied crusts of the Negev Desert (Israel) and the Tengger Desert (China), melanized fungi with large multicellular spores were much less abundantly represented, while the thermotolerant group, Aspergillus spp., remarkably contributed to the communities’ structure. Density of microfungal isolates positively correlated with chlorophyll content indicating possible significant influence of organic matter content on fungal biomass. The variations in crust composition, biomass, and the position of habitats were accompanied by the variations in microfungal community structure, diversity level, and isolate densities, with the communities at the plain sun-exposed position being much less variable than the communities at the north-oriented position. The study shows that microclimatic and edaphic factors play an essential role in the development of crust and noncrust microfungal communities, and their structure can be a sensitive indicator of changing environmental conditions at a microscale.
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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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Podolsky IA, Seppälä S, Lankiewicz TS, Brown JL, Swift CL, O'Malley MA. Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing. Annu Rev Chem Biomol Eng 2019; 10:105-128. [PMID: 30883214 DOI: 10.1146/annurev-chembioeng-060718-030340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Candice L Swift
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Assessment of the Diversity of Fungal Community Composition Associated With Vachellia pachyceras and Its Rhizosphere Soil From Kuwait Desert. Front Microbiol 2019; 10:63. [PMID: 30766519 PMCID: PMC6365840 DOI: 10.3389/fmicb.2019.00063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
This research examined the general soil fungi and AM fungal communities associated with a Lonely Tree species (Vachellia pachyceras) existing in the Sabah Al-Ahmad Natural Reserve located at the Kuwait desert. The goals of the study were to describe the general fungal and AM fungal communities present in the rhizospheric, non-rhizospheric soils and roots of V. pachyceras, respectively, as well as local and non-local V. pachyceras seedlings when grown under standard nursery growing environments. Soil and root samples were analyzed for an array of characteristics including soil physicochemical composition, and culture-independent method termed PCR-cloning, intermediate variable region of rDNA, the large subunit (LSU) and internal transcribed spacer (ITS) region sequence identifications. The results reveal that the fungal phylotypes were classified in four major fungal phyla namely Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblage of fungal analyses showed communities dominated by members of the phylum Ascomycota. The assays also revealed a wealth of incertae sedis fungi, mostly affiliated to uncultured fungi from diverse environmental conditions. Striking difference between rhizosphere and bulk soils communities, with more fungal diversities and Operational Taxonomic Units (OTUs) richness associated with both the field and nursery rhizosphere soils. In contrast, a less diverse fungal community was found in the bulk soil samples. The characterization of AM fungi from the root system demonstrated that the most abundant and diversified group belongs to the family Glomeraceae, with the common genus Rhizophagus (5 phylotypes) and another unclassified taxonomic group (5 phylotypes). Despite the harsh climate that prevails in the Kuwait desert, studied roots displayed the existence of considerable number of AM fungal biota. The present work thus provides a baseline of the fungal and mycorrhizal community associated with rhizosphere and non-rhizosphere soils and roots of only surviving V. pachyceras tree from the Kuwaiti desert and seedlings under nursery growing environments.
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Affiliation(s)
- Majda K. Suleiman
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Kingsley Dixon
- ARC Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Lucy Commander
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Ali M. Quoreshi
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Narayana R. Bhat
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Anitha J. Manuvel
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Mini T. Sivadasan
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
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Grishkan I. Spatiotemporal variations in soil cultivable mycobiota at the Arava desert (Israel) along latitudinal and elevational gradients. AIMS Microbiol 2018; 4:502-521. [PMID: 31294230 PMCID: PMC6604944 DOI: 10.3934/microbiol.2018.3.502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/21/2018] [Indexed: 11/18/2022] Open
Abstract
Regional, local, and seasonal distribution of soil culturable microfungi in the Arava Valley, Israel, was examined along altitudinal and latitudinal gradients. A total of 198 species from 86 genera were isolated using the soil dilution plate method. Melanin-containing species with large multi-cellular spores dominated the majority of microfungal communities, while species with picnidial fruit bodies mostly prevailed in the northern part of the Arava Valley located at 190 m below sea level. Aspergilli (mainly Aspergillus fumigatus) and teleomorphic ascomycetes comprised the basic part of thermotolerant mycobiota obtained at 37 °C. The soil at the northern part of the desert held the highest number of microfungal isolates and, at the same time, was characterized by significantly lower species richness. The open sun-exposed localities harbored a significantly higher number of species than the localities under shrub canopies. Isolate density displayed the opposite trend and was significantly lower in the open than in shrub localities. The mycobiota characteristics such as species composition, contribution of major groupings to mycobiota structure, diversity level, and isolate density showed significant correlations with measured edaphic parameters—organic matter content, water content, pH, and especially, with electrical conductivity. Among the environmental aspects, locality position along altitudinal and latitudinal gradients accompanied by locality type (open sun-exposed or under shrubs), strongly influenced the community's characteristics, thus demonstrating the effect of the unique altitudinal position of the northern part of the Arava Valley as well as the ability of microfungal communities to be sensitive to the microscale environmental variability.
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Affiliation(s)
- Isabella Grishkan
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa 3498838, Israel
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Šimonovičová A, Ferianc P, Vojtková H, Pangallo D, Hanajík P, Kraková L, Feketeová Z, Čerňanský S, Okenicová L, Žemberyová M, Bujdoš M, Pauditšová E. Alkaline Technosol contaminated by former mining activity and its culturable autochthonous microbiota. CHEMOSPHERE 2017; 171:89-96. [PMID: 28006667 PMCID: PMC5267631 DOI: 10.1016/j.chemosphere.2016.11.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 05/31/2023]
Abstract
Technosols or technogenic substrates contaminated by potentially toxic elements as a result of iron mining causes not only contamination of the surrounding ecosystem but may also lead to changes of the extent, abundance, structure and activity of soil microbial community. Microbial biomass were significantly inhibited mainly by exceeding limits of potentially toxic metals as arsenic (in the range of 343-511 mg/kg), copper (in the range of 7980-9227 mg/kg), manganese (in the range of 2417-2670 mg/kg), alkaline and strong alkaline pH conditions and minimal contents of organic nutrients. All of the 14 bacterial isolates, belonged to 4 bacterial phyla, Actinobacteria, Firmicutes; β- and γ-Proteobacteria. Thirteen genera and 20 species of microscopic filamentous fungi were recovered. The most frequently found species belonged to genera Aspergillus (A. clavatus, A. niger, A. flavus, A. versicolor, Aspergillus sp.) with the dominating A. niger in all samples, and Penicillium (P. canescens, P. chrysogenum, P. spinulosum, Penicillium sp.). Fungal plant pathogens occurred in all surface samples. These included Bjerkandera adustata, Bionectria ochloleuca with anamorph state Clonostachys pseudochloleuca, Lewia infectoria, Phoma macrostoma and Rhizoctonia sp.
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Affiliation(s)
- A Šimonovičová
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic.
| | - P Ferianc
- Institut of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - H Vojtková
- Institute of Environmental Engineering, Faculty of Mining and Geology, VŠB - Technical University of Ostrava, Czech Republic
| | - D Pangallo
- Institut of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - P Hanajík
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - L Kraková
- Institut of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Z Feketeová
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - S Čerňanský
- Department of Environmental Ecology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - L Okenicová
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - M Žemberyová
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - M Bujdoš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - E Pauditšová
- Department of Landscape Ecology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
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Johnson RM, Ramond JB, Gunnigle E, Seely M, Cowan DA. Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters. Extremophiles 2017; 21:381-392. [PMID: 28058513 DOI: 10.1007/s00792-016-0911-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/19/2016] [Indexed: 01/31/2023]
Abstract
The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R 2 = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R 2 ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.
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Affiliation(s)
- Riegardt M Johnson
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
| | - Eoin Gunnigle
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Mary Seely
- Gobabeb Research and Training Centre, Walvis Bay, Namibia
- School of Animal, Plant and Environmental Sciences (AP&ES), University of the Witwatersrand, Johannesburg, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, Natural Sciences 2, University of Pretoria, Room 3-20, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
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Hernández-Hernández RM, Roldán A, Caravaca F, Rodriguez-Caballero G, Torres MP, Maestre FT, Alguacil MM. Arbuscular mycorrhizal fungal assemblages in biological crusts from a Neotropical savanna are not related to the dominant perennial Trachypogon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 575:1203-1210. [PMID: 27697347 DOI: 10.1016/j.scitotenv.2016.09.190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Knowledge of the arbuscular mycorrhizal fungal assemblages in the Trachypogon savanna ecosystems is very important to a better understanding of the ecological processes mediated by this soil microbial group that affects multiple ecosystem functions. Considering the hypothesis that the biocrusts can be linked to vegetation through the arbuscular fungi mycelial network, the objectives proposed in this study were to determine (i) whether there are arbuscular mycorrhizal fungi (AMF) in the biocrusts (ii) whether arbuscular mycorrhizal fungal assemblages are linked to the Trachypogon patches, and (iii) whether the composition of the assemblages is related to soil properties affected by microbiological activity. The community structure of the AMF was investigated in three habitats: rhizospheric soil and roots of Trachypogon vestitus, biological soil crusts, and bare soil. The canonical correspondence analysis showed that two soil properties related to enzymatic activity (protease and β-glucosidase) significantly affected the community composition of the AMF. The biocrusts in the Venezuelan savanna are colonized by an AM fungal community linked to that of the bare soil and significantly different from that hosted by the roots of the surrounding T. vestitus, suggesting that assemblages of AMF in biocrusts might be related more closely to those of annual plant species appearing in favorable conditions.
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Affiliation(s)
- R M Hernández-Hernández
- Universidad Simón Rodríguez (USR), Instituto de Estudios Científicos y Tecnológicos IDECYT, Av. Mara Altos del Cují, San Antonio de los Altos, estado Miranda, Apdo 47925, Venezuela
| | - A Roldán
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
| | - F Caravaca
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
| | - G Rodriguez-Caballero
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain
| | - M P Torres
- Departamento de Biología Aplicada, Área de Botánica, Universidad Miguel Hernández, Avda. De la Universidad s/n., 03202 Elche, Alicante, Spain
| | - F T Maestre
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles 28933, Spain
| | - M M Alguacil
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, P.O. Box 164, Campus de Espinardo, 30100 Murcia, Spain.
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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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Shakoor A, Abdullah M, Yousaf B, Amina, Ma Y. Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016:10.1007/s11356-016-7823-6. [PMID: 27771880 DOI: 10.1007/s11356-016-7823-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.
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Affiliation(s)
- Awais Shakoor
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- State-Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Balal Yousaf
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Amina
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Youhua Ma
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China.
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Zhang T, Jia RL, Yu LY. Diversity and distribution of soil fungal communities associated with biological soil crusts in the southeastern Tengger Desert (China) as revealed by 454 pyrosequencing. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.08.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang Y, Aradottir AL, Serpe M, Boeken B. Interactions of Biological Soil Crusts with Vascular Plants. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_19] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Coleine C, Selbmann L, Ventura S, D'Acqui LP, Onofri S, Zucconi L. Fungal Biodiversity in the Alpine Tarfala Valley. Microorganisms 2015; 3:612-24. [PMID: 27682108 PMCID: PMC5023259 DOI: 10.3390/microorganisms3040612] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/29/2015] [Indexed: 12/04/2022] Open
Abstract
Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Stefano Ventura
- Institute of Ecosystem Study, National Research Council of Italy (CNR-ISE), I-50019 Sesto Fiorentino, Italy.
| | - Luigi Paolo D'Acqui
- Institute of Ecosystem Study, National Research Council of Italy (CNR-ISE), I-50019 Sesto Fiorentino, Italy.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
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32
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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: 68] [Impact Index Per Article: 7.6] [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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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: 28] [Impact Index Per Article: 3.1] [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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Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Front Microbiol 2015; 6:277. [PMID: 25926821 PMCID: PMC4396413 DOI: 10.3389/fmicb.2015.00277] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/19/2015] [Indexed: 01/10/2023] Open
Abstract
Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.
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Affiliation(s)
- Ulisses Nunes da Rocha
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Quantitative Microbial Ecology Group, Department of Molecular and Cell Physiology, Faculty of Earth and Life Sciences, VU Amsterdam Amsterdam, Netherlands
| | - Hinsby Cadillo-Quiroz
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
| | - Lara Rajeev
- Lawrence Berkeley National Laboratory, Physical Biosciences Division Berkeley, CA, USA
| | - Niels Klitgord
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Sean Dunn
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Viet Truong
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Mayra Buenrostro
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Ferran Garcia-Pichel
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA ; Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Lawrence Berkeley National Laboratory, Physical Biosciences Division Berkeley, CA, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Department of Environmental Science, Policy and Management, University of California, Berkeley Berkeley, CA, USA
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Vargas-Gastélum L, Romero-Olivares AL, Escalante AE, Rocha-Olivares A, Brizuela C, Riquelme M. Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing. FEMS Microbiol Ecol 2015; 91:fiv044. [PMID: 25877341 DOI: 10.1093/femsec/fiv044] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2015] [Indexed: 12/25/2022] Open
Abstract
Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semi-arid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semi-arid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1940 Operational Taxonomic Units (OTUs) were identified from 362 332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows.
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Affiliation(s)
- Lluvia Vargas-Gastélum
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
| | - Adriana L Romero-Olivares
- Department of Ecology and Evolutionary Biology, University of California-Irvine, 321 Steinhaus Hall, Irvine, CA 92697, USA
| | - Ana E Escalante
- National Laboratory of Sustainability Sciences (LANCIS) Ecology Institute, National Autonomous University of Mexico (UNAM), Tercer Circ. Ext. next to Jardín Botánico, Ciudad Universitaria, 70275, Mexico
| | - Axayácatl Rocha-Olivares
- Department of Biological Oceanography, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
| | - Carlos Brizuela
- Department of Computer Sciences, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
| | - Meritxell Riquelme
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, Baja California, 22860, Mexico
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36
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Wu N, Pan HX, Qiu D, Zhang YM. Feasibility of EPS-producing bacterial inoculation to speed up the sand aggregation in the Gurbantunggut Desert, Northwestern China. J Basic Microbiol 2014; 54:1378-86. [PMID: 25224518 DOI: 10.1002/jobm.201400355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/05/2014] [Indexed: 11/10/2022]
Abstract
Exopolymers are known to be useful in improving sand aggregation and the development of biological soil crusts (BSCs). A facultative bacterium KLBB0001 was isolated from BSCs in the Gurbantunggut Desert in northwestern China. With the strong effective production of extracellular polymeric substances (EPS), this strain exhibits a multifunctional role for sand stabilization and maintenance of water under laboratory conditions. Practical testing of the feasibility of its inoculation to speed up BSC recovery in the field was also conducted in this experiment. This strain stimulated the heterotrophic community assembly in the topsoil layer (0-2 cm) before the commencement of autotrophic cyanobacteria, while also significantly increasing the number of bacteria, actinomycetes, and content of total phosphorus, available nitrogen, and available phosphorus. However, the low nitrogenase activity (NA) (0.57 µmol/h) that was observed caused us to doubt the previous identification as Azotobacter Beijerinck that was based on physiological and biochemical properties. A phylogenetic analysis based on 16S rRNA gene sequences revealed that this strain was a member of the genus Paenibacillus. It exhibited the closest phylogenetic affinity and highest sequence similarity to the strain Paenibacillus mucilaginosus VKPM B-7519 (sequence similarity 99.698%), which is well known as a typical silicate-weathering bacteria that releases lots of nutritional ions from minerals and the soil. Because P. mucilaginosus can excrete carbonic anhydrase (CA) to capture atmospheric CO2 through hydration of CO2 , it is possible that KLBB0001 might use a similar strategy for heterotrophs in the BSCs to sequester CO2 from the air. Because of its potential role in the reestablishment of the BSC ecosystem due to its ability to improve water relations, sand stabilization, and chemical erosion, EPS-producing bacterial inoculation was concluded to be a suitable and effective treatment for BSC recovery, especially in environments with limited water and nutrients.
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Affiliation(s)
- Nan Wu
- 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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Davies LO, Schäfer H, Marshall S, Bramke I, Oliver RG, Bending GD. Light structures phototroph, bacterial and fungal communities at the soil surface. PLoS One 2013; 8:e69048. [PMID: 23894406 PMCID: PMC3716809 DOI: 10.1371/journal.pone.0069048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/04/2013] [Indexed: 02/01/2023] Open
Abstract
The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0–3 mm) and bulk soil (3–12 mm) using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.
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Affiliation(s)
- Lawrence O Davies
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom.
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Garcia-Pichel F, Loza V, Marusenko Y, Mateo P, Potrafka RM. Temperature drives the continental-scale distribution of key microbes in topsoil communities. Science 2013; 340:1574-7. [PMID: 23812714 DOI: 10.1126/science.1236404] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Global warming will likely force terrestrial plant and animal species to migrate toward cooler areas or sustain range losses; whether this is also true for microorganisms remains unknown. Through continental-scale compositional surveys of soil crust microbial communities across arid North America, we observed a latitudinal replacement in dominance between two key topsoil cyanobacteria that was driven largely by temperature. The responses to temperature of enrichment cultures and cultivated strains support this contention, with one cyanobacterium (Microcoleus vaginatus) being more psychrotolerant and less thermotolerant than the other (M. steenstrupii). In view of our data and regional climate predictions, the latter cyanobacterium may replace the former in much of the studied area within the next few decades, with unknown ecological consequences for soil fertility and erodibility.
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Treves H, Raanan H, Finkel OM, Berkowicz SM, Keren N, Shotland Y, Kaplan A. A newly isolatedChlorellasp. from desert sand crusts exhibits a unique resistance to excess light intensity. FEMS Microbiol Ecol 2013; 86:373-80. [DOI: 10.1111/1574-6941.12162] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/05/2013] [Accepted: 06/11/2013] [Indexed: 12/13/2022] Open
Affiliation(s)
- Haim Treves
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus - Givat Ram; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Hagai Raanan
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus - Givat Ram; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Omri M. Finkel
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus - Givat Ram; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Simon M. Berkowicz
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus - Givat Ram; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus - Givat Ram; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Yoram Shotland
- Chemical Engineering; Shamoon College of Engineering; Beer Sheva Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus - Givat Ram; The Hebrew University of Jerusalem; Jerusalem Israel
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Steven B, Gallegos-Graves LV, Belnap J, Kuske CR. Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material. FEMS Microbiol Ecol 2013; 86:101-13. [DOI: 10.1111/1574-6941.12143] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Blaire Steven
- Bioscience Division; Los Alamos National Laboratory; Los Alamos; NM; USA
| | | | - Jayne Belnap
- U.S. Geological Survey; Southwest Biological Science Center; Moab; UT; USA
| | - Cheryl R. Kuske
- Bioscience Division; Los Alamos National Laboratory; Los Alamos; NM; USA
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Wu B, Tian J, Bai C, Xiang M, Sun J, Liu X. The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China. ISME JOURNAL 2013; 7:1299-309. [PMID: 23446835 DOI: 10.1038/ismej.2013.29] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Whether fungal community structure depends more on historical factors or on contemporary factors is controversial. This study used culture-dependent and -independent (polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)) methods to assess the influence of historical and contemporary factors on the distributions of fungi in the wetland sediments at 10 locations along the Changjiang River and at 10 other locations in China. The culture-dependent approach detected greater species diversity (177 operational taxonomic units (OTUs)) than PCR-DGGE analysis (145 OTUs), and the species in the genera of Penicillium (relative frequency=16.8%), Fusarium (15.4%), Aspergillus (7.6%), Trichoderma (5.8%) and Talaromyces (4.2%) were dominant. On the basis of DGGE data, fungal diversity along the Changjiang River increased from upstream to downstream; altitude explained 44.8% of this variation in diversity. And based on the data from all 20 locations, the fungal communities were geographically clustered into three groups: Southern China, Northern China and the Qinghai-Tibetan Plateau. Multivariate regression tree analysis for data from the 20 locations indicated that the fungal community was influenced primarily by location (which explained 61.8% of the variation at a large scale), followed by total potassium (9.4%) and total nitrogen (3.5%) at a local scale. These results are consistent with the concept that geographic distance is the dominant factor driving variation in fungal diversity at a regional scale (1000-4000 km), whereas environmental factors (total potassium and total nitrogen) explain variation in fungal diversity at a local scale (<1000 km).
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Affiliation(s)
- Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Reddy GSN, Garcia-Pichel F. Description of Hymenobacter arizonensis sp. nov. from the southwestern arid lands of the United States of America. Antonie van Leeuwenhoek 2012; 103:321-30. [PMID: 22987249 DOI: 10.1007/s10482-012-9812-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 09/07/2012] [Indexed: 11/25/2022]
Abstract
Strain OR362-8(T) was isolated from a biological soil crust sample collected from the southwestern arid lands of the United States of America, using BG11-PGY medium. Cells of OR362-8(T) were found to be rod shaped; occur singly, as pairs and in groups; non-motile; positive for catalase, oxidase, phosphatase and gelatinase; hydrolyze starch; contain iso-C(15:0), anteiso-C(15:0), iso-C(15:1)G, C(16:1ω5c) and summed feature 3 (C(16:1(ω7c))/iso-C(15:0) 2OH as defined by the MIDI system) as the major fatty acids; and MK-7 as the sole respiratory quinone. A BLAST sequence similarity search using 16S rRNA gene sequence of OR362-8(T) identified Hymenobacter as the nearest genus with a similarity of 90.4-96.9 %. The phylogenetic analyses based on the phenetic methods UPGMA, NJ, ME and DNA parsimony resulted in the clustering of OR362-8(T) with Clade 1 Hymenobacter species represented by Hymenobacter glaciei, Hymenobacter antarcticus, Hymenobacter flocculans, Hymenobacter metalli and Hymenobacter soli with the closest being the Hymenobacter glaciei (96.9 % 16S rRNA gene sequence similarity). Besides the strong phylogentic affiliation, OR362-8(T) also exhibited significant phenotypic and chemotaxonomic differences with the members of Clade 1 Hymenobacter spp. More importantly, the DNA G+C content (mol%) of OR362-8(T) is very high (70 %) compared to the nearest species identified by phylogenetic analysis. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, OR362-8(T) was assigned to a novel species for which we propose here the name Hymenobacter arizonensis sp. nov., with OR362-8(T) (=ATCC BAA 1266(T) = DSM 17860(T) = JCM 13504(T)) as the type strain.
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Affiliation(s)
- Gundlapally S N Reddy
- School of Life Sciences, Arizona State University, Main Campus, Tempe, AZ 85287-4501, USA.
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