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Ramírez C, Cardozo M, López Gastón M, Galdeano E, Collavino M. Plant growth promoting activities of endophytic bacteria from Melia azedarach (Meliaceae) and their influence on plant growth under gnotobiotic conditions. Heliyon 2024; 10:e35814. [PMID: 39170558 PMCID: PMC11337034 DOI: 10.1016/j.heliyon.2024.e35814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
Bacteria that live asymptomatically within plant tissues are known as endophytes. Because of the close relation with the plant host, they have been a matter of interest for application as plant growth promoters. Melia azedarach is a widely distributed medicinal tree with proven insecticidal, antimicrobial, and antiviral activity. The aim of this study was to isolate and characterize endophytic bacteria from M. azedarach and analyze their plant growth promoting activities for the potential application as biological products. Bacteria were isolated from roots and leaves of trees growing in two locations of Northeastern Argentina. The isolates were characterized by repetitive extragenic palindromic sequence PCR and 16S rDNA sequence analysis. The plant growth-promoting activities were assayed in vitro, improvement of plant growth of selected isolates was tested on M. azedarach plantlets, and the effect of selected ACC deaminase producing isolates was tested on tomato seedlings under salt-stress conditions. The highest endophytic bacterial abundance and diversity were obtained from the roots. All isolates had at least one of the assayed plant growth-promoting activities and 80 % of them had antagonistic activity. The most efficient bacteria were Pseudomonas monteilii, Pseudomonas farsensis, Burkholderia sp. and Cupriavidus sp. for phosphate solubilization (2064 μg P ml-1), IAA production (94.7 μg ml-1), siderophore production index (5.5) and ACC deaminase activity (1294 nmol α-ketobutyrate mg-1 h-1). M. azedarach inoculation assays revealed the bacterial growth promotion potential, with Pseudomonas monteilii, Pseudomonas farsensis and Cupriavidus sp. standing out for their effect on leaf area, leaf dry weight, specific leaf area, and total Chl, Mg and N content, with increases of up to 149 %, 58 %, 65 %, 178 %, 76 % and 97.7 %, respectively, compared to NI plants. Efficient ACC deaminase-producing isolates increased stress tolerance of tomato plants under saline condition. Overall, these findings indicate the potential of the endophytic isolates as biostimulant and biocontrol agents.
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Affiliation(s)
- C. Ramírez
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - M. Cardozo
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - M. López Gastón
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - E. Galdeano
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - M.M. Collavino
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
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Sorochkina K, Martens-Habbena W, Reardon CL, Inglett PW, Strauss SL. Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops. FEMS Microbiol Ecol 2024; 100:fiae064. [PMID: 38637314 DOI: 10.1093/femsec/fiae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared a similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared with those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All of the examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared with the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence the bacterial and diazotrophic community composition of any of these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced the community composition and function of these biocrusts.
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Affiliation(s)
- Kira Sorochkina
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States
- Southwest Research and Education Center, University of Florida, Immokalee, FL, United States
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL, United States
| | - Catherine L Reardon
- Soil and Water Conservation Research Unit, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pendleton, OR, United States
| | - Patrick W Inglett
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States
| | - Sarah L Strauss
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States
- Southwest Research and Education Center, University of Florida, Immokalee, FL, United States
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Wang L, Li J, Zhang S, Huang Y, Ouyang Z, Mai Z. Biological soil crust elicits microbial community and extracellular polymeric substances restructuring to reduce the soil erosion on tropical island, South China Sea. MARINE ENVIRONMENTAL RESEARCH 2024; 197:106449. [PMID: 38492504 DOI: 10.1016/j.marenvres.2024.106449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Soil erosion stands as the preeminent environmental concern globally, attaining heightened significance, particularly within islands where land resources prove notably scarce. Biological soil crusts, referred to as biocrusts, assume a pivotal ecological role in soil conservation. Notably, they augment the horizontal stability of the substrate through the exudation of microbial extracellular polymeric substances (EPS), thereby shielding the soil against shear stress, exemplified in the form of water erosion. While extant research has delved into the anti-erosion mechanisms of biocrusts in arid landscapes, a conspicuous lacuna persists in the exploration of coral island environments. In this study, we collected and assessed 30 samples encompassing dark biocrusts, light biocrusts, and bare soil to scrutinize the potential anti-erosion efficacy of tropical coral island biocrusts within the South China Sea. Employing a cohesive strength meter, we quantified soil shear stress across various stages of biocrust development, revealing a discernible enhancement in soil erosion resistance during the formation of biocrusts. Relative to the exposed bare soil, the soil shear stress exhibited an escalation from 0.33 N m-2 to 0.61 N m-2 and 1.31 N m-2 in the light biocrusts and dark biocrusts, respectively. Mechanistically, we assayed microbial EPS contents, exposing a positive correlation between EPS and soil anti-erodibility, encompassing extracellular protein and polysaccharide. Concurrently, bacterial abundance displayed a significant augmentation commensurate with biocrust formation and development. In pursuit of elucidating the origin of EPS, high-throughput amplicon sequencing was executed to identify microorganisms contributing to biocrust development. Correlation analysis discerned Cyanobacteria, Chloroflexi, Deinococcota, and Patescibacteria as potential microbials fostering EPS production and fortifying erosion resistance. Collectively, our study presents the first evidence that biocrust from tropical coral reef island in the South China Sea promotes resistance to soil erosion, pinpointing key EPS-producing microbials against soil erosion. The findings would provide insights for island environment restoration.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong, PR China
| | - Yadong Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Zhiyuan Ouyang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
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Mai Z, Chen Q, Wang L, Zhang J, Cheng H, Su H, Zhang S, Li J. Bacterial carbonic anhydrase-induced carbonates mitigate soil erosion in biological soil crusts. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120085. [PMID: 38219667 DOI: 10.1016/j.jenvman.2024.120085] [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: 09/21/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
Soil erosion is a significant environmental issue worldwide, particularly in island regions where land resources are exceedingly scarce. Biological soil crusts play a crucial role in mitigating soil erosion, yet the precise effect and mechanism of biological soil crusts against erosion remain ambiguous. In this study, biological soil crusts at various developmental stages from a tropical coral island in the South China Sea were chosen to investigate the role of carbonic anhydrase in mitigating erosion. A cohesive strength meter, real-time quantitative PCR, and 16S rRNA gene high-throughput sequencing were employed to assess variations in soil antiscouribility as well as bacterial abundance and composition during the formation and development of biological soil crusts. Scanning electron microscopy was utilized to detect carbonates induced by bacterial carbonic anhydrase and elucidate their role in the solidification of sand particles. The findings indicate that the formation and development of biological soil crusts significantly enhance anti-scouribility. Comparison to those of bare coral sand, the shear stress increased from 0.35 to 1.11 N/m2 in the dark biocrusts. Moreover, significantly elevated carbonic anhydrase activity was observed in biological soil crusts, demonstrating a positive correlation with antiscouribility. In addition, there was a significant increase in bacterial abundance within the biological soil crusts. The enrichment of Cyanobacteriales and Chloroflexales potentially contributed to the increased carbonic anhydrase activity and antiscouribility. Furthermore, three cyanobacterial strains with carbonic anhydrase activity were isolated from biological soil crusts and subsequently confirmed to enhance sand solidification through microbial carbonate precipitation. This study presents initial evidence for the role of microbial carbonic anhydrase in enhancing the antiscouribility of biological soil crusts during their formation and development. These findings offer novel insights into the functional and mechanistic dimensions underlying the mitigation of soil erosion facilitated by biological soil crusts, which are valuable for implementing sustainable biorestoration and environmental management technologies to prevent soil erosion.
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Affiliation(s)
- Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Qiqi Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hao Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hongfei Su
- Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong, China.
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Chowaniec K, Styburski J, Kozioł S, Pisańska Z, Skubała K. Dune Blowouts as Microbial Hotspots and the Changes of Overall Microbial Activity and Photosynthetic Biomass Along with Succession of Biological Soil Crusts. MICROBIAL ECOLOGY 2023; 87:22. [PMID: 38157058 PMCID: PMC10756888 DOI: 10.1007/s00248-023-02333-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Biological soil crust (BSC) constitutes a consortium of cyanobacteria, algae, lichen, mosses, and heterotrophic microorganisms, forming a miniature ecosystem within the uppermost soil layer. The biomass of different organisms forming BSC and their activity changes along with succession. Previous studies focused primarily on BSC in hyper-arid/arid regions, whereas the ecophysiology of BSC in temperate climates is still not well recognized. In order to determine changes in overall microbial activity and photosynthetic biomass in BSC at different stages of the succession of inland sandy grasslands, we analyzed dehydrogenase activity and determined the content of photosynthetic pigments. We also compared these parameters between BSC developed on the dune ridges and aeolian blowouts in the initial stage of succession. Our study revealed a significant increase in both photosynthetic biomass and overall microbial activity in BSC as the succession of inland shifting sands progresses. We found that chl a concentration in BSC could be considered a useful quantitative indicator of both the presence of photoautotrophs and the degree of soil crust development in warm-summer humid continental climates. The photosynthetic biomass was closely related to increased microbial activity in BSC, which suggests that photoautotrophs constitute a major BSC component. Dune blowouts constitute environmental niches facilitating the development of BSC, compared to dune ridges. High biomass of microorganisms in the dune blowouts may be associated with a high amount of organic material and more favorable moisture conditions. We conclude that deflation fields are key places for keeping a mosaic of habitats in the area of shifting sands and can be a reservoir of microorganisms supporting further settlement of dune slopes by BSC.
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Affiliation(s)
- Karolina Chowaniec
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University in Kraków, Prof. S. Łojasiewicza 11, 30-348, Kraków, Poland
| | - Jakub Styburski
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University in Kraków, Prof. S. Łojasiewicza 11, 30-348, Kraków, Poland
| | - Szymon Kozioł
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | - Zofia Pisańska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | - Kaja Skubała
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
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Tang K, Liang Y, Yuan B, Meng J, Feng F. Spatial distribution and core community of diazotrophs in Biological soil crusts and subsoils in temperate semi-arid and arid deserts of China. Front Microbiol 2023; 14:1074855. [PMID: 37608942 PMCID: PMC10440438 DOI: 10.3389/fmicb.2023.1074855] [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: 10/20/2022] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Introduction Biological soil crusts (BSCs) are distributed in arid and semiarid regions, and they function as important microhabitats for nitrogen fixation. The diazotroph community is critical for nitrogen fixation in BSCs and their subsoils. However, little is known about the key groups in different types of BSCs and subsoils in temperate semi-arid or arid deserts. Methods Here, we sampled three types of BSCs and their subsoils from the Inner Mongolian plateau, investigated the distribution characteristics of the diazotroph community by high-throughput sequencing, predicted keystone species using the molecular ecological network analyses pipeline (MENAP), and verified their close relationship with the available nitrogen (AN) content. Results The results showed that available nitrogen content in BSCs was higher than that in subsoils in three different types of BSCs, and there were differences among seasons and according to the mean annual precipitation. The abundance of diazotrophs was higher in Cyano-BSCs, while diversity had no significant difference among BSCs and subsoils. Cyanobacteria and Proteobacteria, Nostocaceae and Scytonemataceae, Skermanella, Scytonema, Azohydromonas, Nostoc and Trichormus were the dominant phyla, families, and genera, respectively. The dominant groups belong to Skermanella, Scytonema, and Nostoc formed the core diazotroph community in the three types of BSCs and subsoils, and each had a close relationship with AN. Discussion These results indicate that diazotrophs in BSCs and subsoils had high diversity, and the core diazotroph communities have a close relationship with nitrogen fixation and that they may be the main contributor to nitrogen fixing in BSCs and subsoils in temperate deserts.
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Affiliation(s)
- Kai Tang
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yungang Liang
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Bo Yuan
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
- College of Life Science, Inner Mongolia Normal University, Hohhot, China
| | - Jianyu Meng
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Fuying Feng
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
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Barrón-Sandoval A, Martiny JBH, Pérez-Carbajal T, Bullock SH, Leija A, Hernández G, Escalante AE. Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system. FEMS Microbiol Ecol 2023; 99:6998555. [PMID: 36690342 PMCID: PMC9923382 DOI: 10.1093/femsec/fiad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.
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Affiliation(s)
- Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 014510, Mexico,Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92627, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92627, United States
| | - Teresa Pérez-Carbajal
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 014510, Mexico
| | - Stephen H Bullock
- Department of Conservation Biology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, 22860 Baja CA, Mexico
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av, Universidad 1001, 62210 Cuernavaca, Morelos, Mexico
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av, Universidad 1001, 62210 Cuernavaca, Morelos, Mexico
| | - Ana E Escalante
- Corresponding author: Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 04510. Mexico. Tel: +52(55)5623-7714; E-mail:
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Employment of algae-based biological soil crust to control desertification for the sustainable development: A mini-review. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Antoninka A, Chuckran PF, Mau RL, Slate ML, Mishler BD, Oliver MJ, Coe KK, Stark LR, Fisher KM, Bowker MA. Responses of Biocrust and Associated Soil Bacteria to Novel Climates Are Not Tightly Coupled. Front Microbiol 2022; 13:821860. [PMID: 35572693 PMCID: PMC9096946 DOI: 10.3389/fmicb.2022.821860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change is expanding drylands even as land use practices degrade them. Representing ∼40% of Earth’s terrestrial surface, drylands rely on biological soil crusts (biocrusts) for key ecosystem functions including soil stability, biogeochemical cycling, and water capture. Understanding how biocrusts adapt to climate change is critical to understanding how dryland ecosystems will function with altered climate. We investigated the sensitivity of biocrusts to experimentally imposed novel climates to track changes in productivity and stability under both warming and cooling scenarios. We established three common gardens along an elevational-climate gradient on the Colorado Plateau. Mature biocrusts were collected from each site and reciprocally transplanted intact. Over 20 months we monitored visible species composition and cover, chlorophyll a, and the composition of soil bacterial communities using high throughput sequencing. We hypothesized that biocrusts replanted at their home site would show local preference, and biocrusts transplanted to novel environments would maintain higher cover and stability at elevations higher than their origin, compared to at elevations lower than their origin. We expected responses of the visible biocrust cover and soil bacterial components of the biocrust community to be coupled, with later successional taxa showing higher sensitivity to novel environments. Only high elevation sourced biocrusts maintained higher biocrust cover and community stability at their site of origin. Biocrusts from all sources had higher cover and stability in the high elevation garden. Later successional taxa decreased cover in low elevation gardens, suggesting successional reversal with warming. Visible community composition was influenced by both source and transplant environment. In contrast, soil bacterial community composition was not influenced by transplant environments but retained fidelity to the source. Thus, responses of the visible and soil bacterial components of the biocrust community were not coupled. Synthesis: Our results suggest biocrust communities are sensitive to climate change, and loss of species and function can be expected, while associated soil bacteria may be buffered against rapid change.
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Affiliation(s)
- Anita Antoninka
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States
| | - Peter F Chuckran
- Department of Biological Sciences, Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, AZ, United States
| | - Rebecca L Mau
- Department of Biological Sciences, Center for Ecosystem Science and Society (ECOSS), Northern Arizona University, Flagstaff, AZ, United States
| | - Mandy L Slate
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Melvin J Oliver
- Interdisciplinary Plant Group, Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Kirsten K Coe
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - Llo R Stark
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, Los Angeles, CA, United States
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, Flagstaff, AZ, United States
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Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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Wang L, Li J, Zhang S. A Comprehensive Network Integrating Signature Microbes and Crucial Soil Properties During Early Biological Soil Crust Formation on Tropical Reef Islands. Front Microbiol 2022; 13:831710. [PMID: 35369528 PMCID: PMC8969229 DOI: 10.3389/fmicb.2022.831710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/15/2022] [Indexed: 11/26/2022] Open
Abstract
Biological soil crusts (BSCs/biocrusts), which are distributed across various climatic zones and well-studied in terrestrial drylands, harbor polyextremotolerant microbial topsoil communities and provide ecological service for local and global ecosystem. Here, we evaluated BSCs in the tropical reef islands of the South China Sea. Specifically, we collected 41 BSCs, subsurface, and bare soil samples from the Xisha and Nansha Archipelagos. High-throughput amplicon sequencing was performed to analyze the bacterial, fungal, and archaeal compositions of these samples. Physicochemical measurement and enzyme activity assays were conducted to characterize the soil properties. Advanced computational analysis revealed 47 biocrust-specific microbes and 10 biocrust-specific soil properties, as well as their correlations in BSC microbial community. We highlighted the previously underestimated impact of manganese on fungal community regulation and BSC formation. We provide comprehensive insight into BSC formation networks on tropical reef islands and established a foundation for BSC-directed environmental restoration.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Jie Li,
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Si Zhang,
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12
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Garby TJ, Jordan M, Timms V, Walter MR, Neilan BA. 2-Methylhopanoids in geographically distinct, arid biological soil crusts are primarily cyanobacterial in origin. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:164-169. [PMID: 34898023 DOI: 10.1111/1758-2229.13037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/10/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Microbial palaeontology is largely reliant on the interpretation of geologically stable biomarkers or molecular fossils. Biomolecules that are both specific to particular groups of organisms and stable on a geological scale are invaluable for tracing the emergence and diversification of lifeforms, particularly in cases where mineral fossils are lacking. 2-Methylhopanoids and their diagenic product, 2-methylhopanes, are highly abundant bacterial membrane lipids, recoverable from samples in excess of a billion years old. In this work we used degenerate PCR, targeting 2-methylhopanoid biosynthesis genes, and sequencing to show that the ability to produce these molecules in arid biological soil crusts from deserts in diverse geographical locations (Utah, USA, and the Pilbara, Australia) is largely confined to cyanobacteria. These data suggest that 2-methylhopanes can be used as a proxy for cyanobacterial presence within these environments, contributing to our understanding of the emergence of terrestrial life on Earth.
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Affiliation(s)
- Tamsyn J Garby
- Australian Centre for Astrobiology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew Jordan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Verlaine Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Malcolm R Walter
- Australian Centre for Astrobiology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
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13
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Séneca J, Söllinger A, Herbold CW, Pjevac P, Prommer J, Verbruggen E, Sigurdsson BD, Peñuelas J, Janssens IA, Urich T, Tveit AT, Richter A. Increased microbial expression of organic nitrogen cycling genes in long-term warmed grassland soils. ISME COMMUNICATIONS 2021; 1:69. [PMID: 36759732 PMCID: PMC9723740 DOI: 10.1038/s43705-021-00073-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/26/2021] [Accepted: 11/05/2021] [Indexed: 11/08/2022]
Abstract
Global warming increases soil temperatures and promotes faster growth and turnover of soil microbial communities. As microbial cell walls contain a high proportion of organic nitrogen, a higher turnover rate of microbes should also be reflected in an accelerated organic nitrogen cycling in soil. We used a metatranscriptomics and metagenomics approach to demonstrate that the relative transcription level of genes encoding enzymes involved in the extracellular depolymerization of high-molecular-weight organic nitrogen was higher in medium-term (8 years) and long-term (>50 years) warmed soils than in ambient soils. This was mainly driven by increased levels of transcripts coding for enzymes involved in the degradation of microbial cell walls and proteins. Additionally, higher transcription levels for chitin, nucleic acid, and peptidoglycan degrading enzymes were found in long-term warmed soils. We conclude that an acceleration in microbial turnover under warming is coupled to higher investments in N acquisition enzymes, particularly those involved in the breakdown and recycling of microbial residues, in comparison with ambient conditions.
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Affiliation(s)
- Joana Séneca
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Judith Prommer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Erik Verbruggen
- Research Group PLECO, Department of Biology, University of Antwerp, Antwerp, Belgium
| | | | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF- CSIC-UAB, Bellaterra, Catalonia, Spain
| | - Ivan A Janssens
- Research Group PLECO, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Tim Urich
- Department of Bacterial Physiology, University of Greifswald, Greifswald, Germany
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
- Austrian Polar Research Institute, Vienna, Austria.
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14
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Beneficial cyanosphere heterotrophs accelerate establishment of cyanobacterial biocrust. Appl Environ Microbiol 2021; 87:e0123621. [PMID: 34379492 DOI: 10.1128/aem.01236-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological soil crusts (biocrusts) are communities of microbes that inhabit the surface of arid soils and provide essential services to dryland ecosystems. While resistant to extreme environmental conditions, biocrusts are susceptible to anthropogenic disturbances that can deprive ecosystems of these valuable services for decades. Until recently, culture-based efforts to produce inoculum for cyanobacterial biocrust restoration in the Southwestern US focused on producing and inoculating the most abundant primary producers and biocrust pioneers, Microcoleus vaginatus and members of the family Coleofasciculaceae (aka "Microcoleus streenstrupii complex"). The discovery that a unique microbial community characterized by diazotrophs is intimately associated with M. vaginatus, known as the "cyanosphere", suggests a symbiotic division of labor in which nutrients are traded between phototrophs and heterotrophs. To probe the potential use of such cyanosphere members in the restoration of biocrusts, we performed co-inoculations of soil substrates with cyanosphere constituents. This resulted in more rapid cyanobacterial growth over inoculations with the cyanobacterium alone. Additionally, we found that the mere addition of beneficial heterotrophs enhanced the formation of a cohesive biocrust without the need of additional phototrophic biomass within native soils that contain trace amounts of biocrust cyanobacteria. Our findings support the hitherto unknown role of beneficial heterotrophic bacteria in the establishment and growth of biocrusts and allow us to make recommendations concerning biocrust restoration efforts based on the presence of remnant biocrust communities in disturbed areas. Future biocrust restoration efforts should consider cyanobacteria and their beneficial heterotrophic community as inoculants. Importance The advancement of biocrust restoration methodologies for cyanobacterial biocrusts has been largely achieved through trial and error. Successes and failures could not always be traced back to particular factors. The investigation and application of foundational microbial interactions existing within biocrust communities is a crucial step toward informed and repeatable biocrust restoration methodologies.
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15
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Nejidat A, Diaz-Reck D, Gelfand I, Zaady E. Persistence and spread of tetracycline resistance genes and microbial community variations in the soil of animal corrals in a semi-arid planted forest. FEMS Microbiol Ecol 2021; 97:6323997. [PMID: 34279614 DOI: 10.1093/femsec/fiab106] [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] [Received: 12/29/2020] [Accepted: 07/15/2021] [Indexed: 11/14/2022] Open
Abstract
At the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1-10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23-26%) than in the other corrals and the control (33-38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1-10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.
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Affiliation(s)
- Ali Nejidat
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel
| | - Damiana Diaz-Reck
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-G urion 84990, Israel
| | - Ilya Gelfand
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 84990, Israel
| | - Eli Zaady
- Department of Natural Resources, Gilat Research Center, Agriculture Research Organization, Mobile, Post Negev 8531100, Israel
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16
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Tang K, Yuan B, Jia L, Pan X, Feng F, Jin K. Spatial and temporal distribution of aerobic anoxygenic phototrophic bacteria: key functional groups in biological soil crusts. Environ Microbiol 2021; 23:3554-3567. [PMID: 33687799 DOI: 10.1111/1462-2920.15459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/07/2021] [Indexed: 11/27/2022]
Abstract
Several significant ecosystem services are performed by biological soil crusts (BSCs) in drylands, wherein photoautotrophic microorganisms are commonly critical contributors. However, aerobic anoxygenic phototrophic bacteria (AAnPB) are rarely reported in BSCs, despite being the second major branch of Earth's phototrophic microbes. Here, we collected different types of BSCs and their subsoils from temperate deserts, investigated distributions of AAnPB communities among BSCs using cultivation and high-throughput sequencing approaches, predicted keystone species by co-occurrence network analysis, and verified their effects on BSCs formation through microcosm experiments. The absolute abundances and diversity of AAnPB were higher in BSCs and were closely related with BSCs successional stages, as well as soil organic carbon contents. AAnPB communities in both BSCs and their subsoils were dominated by Proteobacteria and Alphaproteobacteria, specifically Acetobacteraceae, Rhodospirillaceae, Roseiflexaceae, Sphingomonadaceae and Caulobacteraceae families. Mean annual precipitation, pH and available nutrients were the primary factors that shaped AAnPB community structures. The predicted keystone species belonged to the families Acetobacteraceae, Rhodospirillaceae and Sphingomonadanceae. Microcosm experiments demonstrated that inoculation with strains from the three families greatly accelerated the formation and development of BSCs. These observations suggest that AAnPB are likely important functional groups in BSCs that significantly contribute to their formation and important ecosystem services.
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Affiliation(s)
- Kai Tang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Grassland Ecology and Restoration, Ministry of Agriculture, Hohhot, 010010, China.,Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Bo Yuan
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.,College of Life Science, Inner Mongolia Normal University, Hohhot, 010018, China
| | - Lijuan Jia
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Grassland Ecology and Restoration, Ministry of Agriculture, Hohhot, 010010, China.,Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xin Pan
- College of Computer and information Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Fuying Feng
- Institute for Applied and Environmental Microbiology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Ke Jin
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Grassland Ecology and Restoration, Ministry of Agriculture, Hohhot, 010010, China
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17
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Wang Y, Chen Y, Xue Q, Xiang Q, Zhao K, Yu X, Chen Q, Ma M, Jiang H, Zhang X, Penttinen P, Gu Y. The Abundance of the nifH Gene Became Higher and the nifH-Containing Diazotrophic Bacterial Communities Changed During Primary Succession in the Hailuogou Glacier Chronosequence, China. Front Microbiol 2021; 12:672656. [PMID: 34135879 PMCID: PMC8200853 DOI: 10.3389/fmicb.2021.672656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
Primary successional ecosystems and the related soil development are often N limited. To date, N2-fixing communities during primary succession in alpine ecosystems have remained underexplored. In this study, we applied quantitative PCR (qPCR) quantitation and targeted amplicon sequencing of nifH in the Hailuogou Glacier foreland to investigate the succession of N2-fixing communities in five sites along a 62-year chronosequence. The abundance of the nifH gene increased along the primary succession in the chronosequence and correlated positively with pH, acetylene reduction activity, and water, organic C, total and available N, and available P contents. The increases in alpha diversity along the chronosequence may have been partly due to less competition for resources. In contrast to the clear separation based on soil properties, the changes in the diazotrophic community composition lacked a clear trend and were associated mostly with changes in soil available K and organic C contents. The changes among differentially abundant genera were possibly due to the changes in plant coverage and species composition. The whole primary succession of the diazotrophic communities was consistent with stochastic community assembly, which is indicative of low competitive pressure.
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Affiliation(s)
- Yingyan Wang
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yulan Chen
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qinyu Xue
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hao Jiang
- Institute of Chengdu Mountain Hazards and Environment, Chinese Academy Sciences, Chengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
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18
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Consequences of Piñon-Juniper Woodland Fuel Reduction: Prescribed Fire Increases Soil Erosion While Mastication Does Not. Ecosystems 2021. [DOI: 10.1007/s10021-021-00644-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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You Y, Aho K, Lohse KA, Schwabedissen SG, Ledbetter RN, Magnuson TS. Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem. Front Microbiol 2021; 12:569791. [PMID: 34025590 PMCID: PMC8134670 DOI: 10.3389/fmicb.2021.569791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.
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20
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Algal Toxic Compounds and Their Aeroterrestrial, Airborne and other Extremophilic Producers with Attention to Soil and Plant Contamination: A Review. Toxins (Basel) 2021; 13:toxins13050322. [PMID: 33946968 PMCID: PMC8145420 DOI: 10.3390/toxins13050322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
The review summarizes the available knowledge on toxins and their producers from rather disparate algal assemblages of aeroterrestrial, airborne and other versatile extreme environments (hot springs, deserts, ice, snow, caves, etc.) and on phycotoxins as contaminants of emergent concern in soil and plants. There is a growing body of evidence that algal toxins and their producers occur in all general types of extreme habitats, and cyanobacteria/cyanoprokaryotes dominate in most of them. Altogether, 55 toxigenic algal genera (47 cyanoprokaryotes) were enlisted, and our analysis showed that besides the “standard” toxins, routinely known from different waterbodies (microcystins, nodularins, anatoxins, saxitoxins, cylindrospermopsins, BMAA, etc.), they can produce some specific toxic compounds. Whether the toxic biomolecules are related with the harsh conditions on which algae have to thrive and what is their functional role may be answered by future studies. Therefore, we outline the gaps in knowledge and provide ideas for further research, considering, from one side, the health risk from phycotoxins on the background of the global warming and eutrophication and, from the other side, the current surge of interest which phycotoxins provoke due to their potential as novel compounds in medicine, pharmacy, cosmetics, bioremediation, agriculture and all aspects of biotechnological implications in human life.
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21
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Meier DV, Imminger S, Gillor O, Woebken D. Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. mSystems 2021; 6:e00786-20. [PMID: 33436509 PMCID: PMC7901476 DOI: 10.1128/msystems.00786-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.
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Affiliation(s)
- Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stefanie Imminger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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22
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Reis CRG, Pacheco FS, Reed SC, Tejada G, Nardoto GB, Forti MC, Ometto JP. Biological nitrogen fixation across major biomes in Latin America: Patterns and global change effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140998. [PMID: 32763600 DOI: 10.1016/j.scitotenv.2020.140998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Biological nitrogen fixation (BNF) supports terrestrial primary productivity and plays key roles in mediating human-induced changes in global nitrogen (N) and carbon cycling. However, there are still critical uncertainties in our understanding of the amount of BNF occurring across terrestrial ecosystems, and of how terrestrial BNF will respond to global change. We synthesized BNF data from Latin America, a region reported to sustain some of the highest BNF rates on Earth, but that is underrepresented in previous data syntheses. We used meta-analysis and modeling approaches to estimate BNF rates across Latin America's major biomes and to evaluate the potential effects of increased N deposition and land-use change on these rates. Unmanaged tropical and subtropical moist forests sustained observed and predicted total BNF rates of 10 ± 1 and 14 ± 1 kg N ha-1 y-1, respectively, supporting the hypothesis that these forests sustain lower BNF rates than previously thought. Free-living BNF accounted for two-thirds of the total BNF in these forests. Despite an average 30% reduction of free-living BNF in response to experimental N-addition, our results suggest free-living BNF rate responses to current and projected N deposition across tropical and subtropical moist forests are small. In contrast, the conversion of unmanaged ecosystems to crop and pasture lands increased BNF rates across all terrestrial biomes, mostly in savannas, grasslands, and dry forests, increasing BNF rates 2-fold. The information obtained here provides a more comprehensive understanding of BNF patterns for Latin America.
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Affiliation(s)
- Carla R G Reis
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil.
| | - Felipe S Pacheco
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, 2290, S.W. Resource Blvd, Moab, UT 84532, USA
| | - Graciela Tejada
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
| | - Gabriela B Nardoto
- Department of Ecology, Campus Darcy Ribeiro, University of Brasilia, Brasilia, Federal District 70910-900, Brazil
| | - Maria C Forti
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
| | - Jean P Ometto
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
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Tucker C, Ferrenberg S, Reed SC. Modest Residual Effects of Short-Term Warming, Altered Hydration, and Biocrust Successional State on Dryland Soil Heterotrophic Carbon and Nitrogen Cycling. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.467157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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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Effect of soil chemical fertilization on the diversity and composition of the tomato endophytic diazotrophic community at different stages of growth. Braz J Microbiol 2020; 51:1965-1975. [PMID: 32895888 DOI: 10.1007/s42770-020-00373-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/02/2020] [Indexed: 10/23/2022] Open
Abstract
The aim of this work was to gain a more comprehensive and perspicacious view of the endophytic diazotrophic community (EDC) of tomato plant bacteria and assess the effects of chemical fertilization and the plant phenologic stage on the status of those microbes. When the EDC of stem and roots from tomato plants grown in a greenhouse with and without exogenous chemical fertilization was examined by pyrosequencing the nifH gene during the growth cycle, a high taxonomic and phylogenetic diversity was observed. The abundant taxa were related to ubiquitous endophytes such as Rhizobium or Burkholderia but also involved anaerobic members usually restricted to flooded plant tissues, such as Clostridium, Geobacter, and Desulfovibrio. The EDC composition appeared to be dynamic during the growth phase of the tomato, with the structure of the community at the early stages of growth displaying major differences from the late stages. Inorganic fertilization negatively affected the diversity and modified the profile of the predominant components of the EDC in the different growth stages. Populations such as Burkholderia and Geobacter plus the Cyanobacteria appeared particularly affected by fertilization.Our work demonstrates an extensive endophytic diazotrophic diversity, suggesting a high potential for nitrogen fixation. The effect of the phenologic stage and inorganic-chemical soil fertilization on the community structure indicated a dynamic community that responded to environmental changes. These findings contribute to a better understanding of endophytic associations that could be helpful in assisting to shape the endomicrobiome that provides essential benefits to crops.
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Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation. Appl Environ Microbiol 2020; 86:AEM.00195-20. [PMID: 32169937 DOI: 10.1128/aem.00195-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.
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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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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: 11] [Impact Index Per Article: 2.8] [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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Fick SE, Day N, Duniway MC, Hoy‐Skubik S, Barger NN. Microsite enhancements for soil stabilization and rapid biocrust colonization in degraded drylands. Restor Ecol 2019. [DOI: 10.1111/rec.13071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephen E. Fick
- US Geological Survey Southwest Biological Science Center Moab UT U.S.A
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO U.S.A
| | - Natalie Day
- US Geological Survey Southwest Biological Science Center Moab UT U.S.A
| | | | - Sean Hoy‐Skubik
- US Geological Survey Southwest Biological Science Center Moab UT U.S.A
| | - Nichole N. Barger
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO U.S.A
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The Soil Microbiome of the Laurel Forest in Garajonay National Park (La Gomera, Canary Islands): Comparing Unburned and Burned Habitats after a Wildfire. FORESTS 2019. [DOI: 10.3390/f10121051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The evergreen laurel forest is a relic of ancient subtropical/tropical forests, of which the best remnant in the Canary Islands is in Garajonay National Park, on La Gomera island. The soil microbiome associated with a mature undisturbed (unburned) laurel forest was characterized at two locations at different topographical positions on the mountain: The slope and the ridge crest. Given the unusual circumstance of an intense wildfire that severely affected part of this forest, the burned soils were also studied. The soil in undisturbed areas was relatively uniform. The bacterial community composition was dominated by bacteria from phyla Proteobacteria, Acidobacteria, and Actinobacteria. The wildfire changed the composition of the bacterial communities. The Acidobacteria, Actinobacteria, and Alphaproteobacteria (dominant class in unburned forests) significantly decreased in burned soils along with a parallel high increase in Betaproteobacteria, Bacteroidetes, and Firmicutes. We further showed the dramatic effect of a wildfire on the soil microbiome of the laurel forest, appearing as a loss of species richness and diversity, species dominance, and changes in the composition of the bacterial communities.
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Moreira-Grez B, Tam K, Cross AT, Yong JWH, Kumaresan D, Nevill P, Farrell M, Whiteley AS. The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil. Front Microbiol 2019; 10:2143. [PMID: 31608023 PMCID: PMC6768011 DOI: 10.3389/fmicb.2019.02143] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 08/30/2019] [Indexed: 02/01/2023] Open
Abstract
Biocrusts are aggregated crusts that exist on the soil surface of arid environments. They are complex microbial communities comprised of cyanobacteria, lichens, mosses, algae and fungi. Recently, biocrusts have gained significant attention due to their ubiquitous distribution and likely important ecological roles, including soil stabilization, soil moisture retention, carbon (C) and nitrogen (N) fixation, as well as microbial engineers for semi-arid ecosystem restoration. Here, we collected three co-occurring types of biocrust (Cyanobacterial crust, Crustose lichen, and Foliose lichen) and their underlying soil from arid zones within Western Australia. Bacterial microbiome composition was determined through 16S rRNA gene amplicon sequencing to assess the extent of microbiome selection within the crusts versus underlying soil and biogeochemical measures performed to determine whether the crusts had significant impact upon the underlying soil for nutrient input. We determined that the bacterial communities of native biocrusts are distinct from those in their underlying soil, where dominant bacterial taxa differed according to crust morphologies. δ15N revealed that N-fixation appeared most evident in Foliose lichen crust (1.73 ± 1.04‰). Consequently, depending upon the crust type, biocrusts contained higher concentrations of organic C (2 to 50 times), total N (4 to 16 times) and available ammonium (2 to 4 times), though this enrichment did not extend to the soils underneath them. These findings demonstrate that biocrust communities are seemingly islands of biological activity in an arid landscape, uniquely different from their surrounding and underlying soil.
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Affiliation(s)
- Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
| | - Kang Tam
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Adam T. Cross
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Jean W. H. Yong
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
- School of Biological Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Deepak Kumaresan
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paul Nevill
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Mark Farrell
- CSIRO Agriculture and Food, Urrbrae, SA, Australia
| | - Andrew S. Whiteley
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
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Jung P, Briegel-Williams L, Schermer M, Büdel B. Strong in combination: Polyphasic approach enhances arguments for cold-assigned cyanobacterial endemism. Microbiologyopen 2018; 8:e00729. [PMID: 30239166 PMCID: PMC6528576 DOI: 10.1002/mbo3.729] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 11/24/2022] Open
Abstract
Cyanobacteria of biological soil crusts (BSCs) represent an important part of circumpolar and Alpine ecosystems, serve as indicators for ecological condition and climate change, and function as ecosystem engineers by soil stabilization or carbon and nitrogen input. The characterization of cyanobacteria from both polar regions remains extremely important to understand geographic distribution patterns and community compositions. This study is the first of its kind revealing the efficiency of combining denaturing gradient gel electrophoresis (DGGE), light microscopy and culture‐based 16S rRNA gene sequencing, applied to polar and Alpine cyanobacteria dominated BSCs. This study aimed to show the living proportion of cyanobacteria as an extension to previously published meta‐transcriptome data of the same study sites. Molecular fingerprints showed a distinct clustering of cyanobacterial communities with a close relationship between Arctic and Alpine populations, which differed from those found in Antarctica. Species richness and diversity supported these results, which were also confirmed by microscopic investigations of living cyanobacteria from the BSCs. Isolate‐based sequencing corroborated these trends as cold biome clades were assigned, which included a potentially new Arctic clade of Oculatella. Thus, our results contribute to the debate regarding biogeography of cyanobacteria of cold biomes.
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Affiliation(s)
- Patrick Jung
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, Kaiserslautern, Germany
| | - Laura Briegel-Williams
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, Kaiserslautern, Germany
| | - Michael Schermer
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, Kaiserslautern, Germany
| | - Burkhard Büdel
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, Kaiserslautern, Germany
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Yu Y, Zhang J, Petropoulos E, Baluja MQ, Zhu C, Zhu J, Lin X, Feng Y. Divergent Responses of the Diazotrophic Microbiome to Elevated CO 2 in Two Rice Cultivars. Front Microbiol 2018; 9:1139. [PMID: 29910783 PMCID: PMC5992744 DOI: 10.3389/fmicb.2018.01139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/14/2018] [Indexed: 01/20/2023] Open
Abstract
The species-specific responses of plant growth to elevated atmospheric CO2 concentration (eCO2) could lead to N limitation and potentially influence the sustainability of ecosystem. Questions remain unanswered with regards to the response of soil N2-fixing community to eCO2 when developing high-yielding agroecosystem to dampen the future rate of increase in CO2 levels and associated climate warming. This study demonstrates the divergent eCO2 influences on the paddy diazotrophic community between weak- and strong-responsive rice cultivars. In response to eCO2, the diazotrophic abundance increased more for the strong-responsive cultivar treatments than for the weak-responsive ones. Only the strong-responsive cultivars decreased the alpha diversity and separated the composition of diazotrophic communities in response to eCO2. The topological indices of the ecological networks further highlighted the different co-occurrence patterns of the diazotrophic microbiome in rice cultivars under eCO2. Strong-responsive cultivars destabilized the diazotrophic community by complicating and centralizing the co-occurrence network as well as by shifting the hub species from Bradyrhizobium to Dechloromonas in response to eCO2. On the contrary, the network pattern of the weak-responsive cultivars was simplified and decentralized in response to eCO2, with the hub species shifting from Halorhodospira under aCO2 to Sideroxydans under eCO2. Collectively, the above information indicates that the strong-responsive cultivars could potentially undermine the belowground ecosystem from the diazotrophs perspective in response to eCO2. This information highlights that more attention should be paid to the stability of the belowground ecosystem when developing agricultural strategies to adapt prospective climatic scenarios by growing high-yielding crop cultivars under eCO2.
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Affiliation(s)
- Yongjie Yu
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | | | - Marcos Q. Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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Srivastava M, Mishra AK. Comparative responses of diazotrophic abundance and community structure to the chemical composition of paddy soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:399-412. [PMID: 29039042 DOI: 10.1007/s11356-017-0375-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
Diazotrophy is considered as one of the most crucial and dynamic phenomena in the rice field and also a major source of nitrogen input. The objective of this study was to elucidate possible interactions between diverse and dominant diazotrophic bacterial community and organic carbon composition of the paddy soil. Our results suggest that most abundantly found diazotrophs belong to a proteobacteria group and uncultured bacterial forms. A gene abundance study clearly showed significantly higher diazotrophic abundance (P < 0.01) at Chandauli (CHN) as compared to Varanasi (VNS) and Ghazipur (GHJ) districts of Eastern Uttar Pradesh, India, with nitrogenase reductase (nifH) copy number between 1.44 × 103 and 3.34 × 103 copy g-1 soil. Fourier-transform infrared (FT-IR) spectroscopy data identified -CO-, C=O ([Formula: see text] and -NH-), [Formula: see text], and OH- as dominant organic functional groups in the paddy soil. Multivariate analysis was performed to get a clear and more accurate picture of interactions between free-living diazotrophs and abiotic soil factors. Regression analysis suggested a similar trend of distribution of different functional groups along each site. Relative abundance and diversity of diazotrophic population increased in response to FT-IR-based soil organic fractions. Maximum number of FT-IR spectral peak at sites in the Chandauli district augmented its bacterial diazotrophic diversity and abundance. Taken together, the present study sheds light on the substrate-driven composition of the microbial population of selected paddy areas.
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Affiliation(s)
- Meenakshi Srivastava
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
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36
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Mogul R, Vaishampayan P, Bashir M, McKay CP, Schubert K, Bornaccorsi R, Gomez E, Tharayil S, Payton G, Capra J, Andaya J, Bacon L, Bargoma E, Black D, Boos K, Brant M, Chabot M, Chau D, Cisneros J, Chu G, Curnutt J, DiMizio J, Engelbrecht C, Gott C, Harnoto R, Hovanesian R, Johnson S, Lavergne B, Martinez G, Mans P, Morales E, Oei A, Peplow G, Piaget R, Ponce N, Renteria E, Rodriguez V, Rodriguez J, Santander M, Sarmiento K, Scheppelmann A, Schroter G, Sexton D, Stephenson J, Symer K, Russo-Tait T, Weigel B, Wilhelm MB. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert. Front Microbiol 2017; 8:1974. [PMID: 29109701 PMCID: PMC5660283 DOI: 10.3389/fmicb.2017.01974] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 02/01/2023] Open
Abstract
In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439) and genus (p < 0.006) levels, including multiple biochemical and geochemical trends (p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Parag Vaishampayan
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Blue Marble Space Institute of Science, Seattle, WA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Mina Bashir
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Chris P McKay
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States
| | - Keith Schubert
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, Baylor University, Waco, TX, United States
| | - Rosalba Bornaccorsi
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,SETI Institute, Mountain View, CA, United States
| | - Ernesto Gomez
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, California State University, San Bernardino, San Bernardino, CA, United States
| | - Sneha Tharayil
- College of Education, University of Texas at Austin, Austin, TX, United States.,Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoffrey Payton
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Orchard Academies 2B: Arts and Media, Bell, CA, United States
| | - Juliana Capra
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Foothills Middle School, Arcadia, CA, United States
| | - Jessica Andaya
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Leonard Bacon
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Maple Hill High School, Castleton-on-Hudson, NY, United States
| | - Emily Bargoma
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - David Black
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,American Academy of Innovation, Jordan, UT, United States
| | - Katie Boos
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michaela Brant
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michael Chabot
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Danny Chau
- Orchard Academies 2B: Arts and Media, Bell, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica Cisneros
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoff Chu
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jane Curnutt
- Department of Computer Science, Baylor University, Waco, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica DiMizio
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Christian Engelbrecht
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Caroline Gott
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Raechel Harnoto
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Ruben Hovanesian
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Shane Johnson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Britne Lavergne
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Gabriel Martinez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Paul Mans
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Ernesto Morales
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Gary Peplow
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Smiley Elementary School, Redlands, CA, United States
| | - Ryan Piaget
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Nicole Ponce
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Eduardo Renteria
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Monica Santander
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Khamille Sarmiento
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Allison Scheppelmann
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Gavin Schroter
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Devan Sexton
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jenin Stephenson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Kristin Symer
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Tatiane Russo-Tait
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Bill Weigel
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Mary B Wilhelm
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
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37
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Kumar M, van Elsas JD, Nissinen R. Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia. Front Microbiol 2017; 8:1972. [PMID: 29081767 PMCID: PMC5645501 DOI: 10.3389/fmicb.2017.01972] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022] Open
Abstract
Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization. Nitrogen fixing bacteria are likely important for plant growth in these habitats, but very little is known of these bacteria or forces shaping their communities. In this study, we characterized the potential nitrogen fixing bacterial (PNFB) communities associated with two arcto-alpine pioneer plant species, Oxyria digyna (mountain sorrel) and Saxifraga oppositifolia (blue saxifrage), in three climate regions. Both of these plants readily colonize low nutrient mineral soils. Our goal was to investigate how climate (region) and, on the other hand, host plant and plant species shape these communities. To our knowledge, this is the first comprehensive study describing PNFB communities associated with pioneer plants in different arcto-alpine biomes. Replicate samples were taken from two arctic regions, Kilpisjärvi and Ny-Ålesund, and one alpine region, Mayrhofen. In these, the PNFB communities in the bulk and rhizosphere soils and the plant endospheres were characterized by nifH-targeted PCR and massive parallel sequencing. The data revealed strong effects of climatic region on the dominating nitrogen fixers. Specifically, nifH sequences related to Geobacter (δ-Proteobacteria) were present in high relative abundances in the nitrogen-fixing communities in the Mayrhofen and Kilpisjärvi regions, while members of the Clostridiales prevailed in the Kilpisjärvi and Ny-Ålesund regions. The bulk and rhizosphere soil as well as the endosphere communities in the Mayrhofen region were all characterized by high relative abundances of nifH sequences related to Geobacter. In contrast, the endosphere and soil (bulk or rhizosphere soil) communities in the High Arctic were highly divergent: endosphere communities in the arctic regions were shaped by Clostridium spp., while nifH sequences representing δ-Proteobacteria, β-Proteobacteria, Cyanobacteria (in Ny-Ålesund), and Verrucomicrobia (in Kilpisjärvi) dominated the soil communities. Interestingly, the major PNFB genera identified in this study have been previously identified as members of conserved core microbiomes in the endospheres and seeds of these plants by 16S rRNA gene based analyses combined with bacterial isolation, suggesting a very tight interaction between diazotrophic bacteria and these arctic pioneer plants. Overall, anaerobic bacterial taxa dominated the PNFB communities of the endospheres and rhizospheres of the two plant species in all study sites. This could indicate anoxic conditions in and around plant roots at the time of sampling (early growth season), created by melting snow and underlying permafrost.
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Affiliation(s)
- Manoj Kumar
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Microbial Ecology, University of Groningen, Groningen, Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, University of Groningen, Groningen, Netherlands
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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38
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Williams L, Jung P, Zheng LJ, Maier S, Peer T, Grube M, Weber B, Büdel B. Assessing recovery of biological soil crusts across a latitudinal gradient in Western Europe. Restor Ecol 2017. [DOI: 10.1111/rec.12579] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Laura Williams
- Plant Ecology and Systematics, Biology Institute; University of Kaiserslautern; PO Box 3049, 67653 Kaiserslautern Germany
| | - Patrick Jung
- Plant Ecology and Systematics, Biology Institute; University of Kaiserslautern; PO Box 3049, 67653 Kaiserslautern Germany
| | - Ling-Juan Zheng
- FB Organismische Biologie; University of Salzburg; Hellbrunnerstrasse 34, 5020 Salzburg Austria
| | - Stefanie Maier
- Institute of Plant Sciences; University of Graz; 8010 Graz Austria
- Multiphase Chemistry Department; Max Planck Institute for Chemistry; Hahn-Meitner-Weg 1, 55128 Mainz Germany
| | - Thomas Peer
- FB Organismische Biologie; University of Salzburg; Hellbrunnerstrasse 34, 5020 Salzburg Austria
| | - Martin Grube
- Institute of Plant Sciences; University of Graz; 8010 Graz Austria
| | - Bettina Weber
- Multiphase Chemistry Department; Max Planck Institute for Chemistry; Hahn-Meitner-Weg 1, 55128 Mainz Germany
| | - Burkhard Büdel
- Plant Ecology and Systematics, Biology Institute; University of Kaiserslautern; PO Box 3049, 67653 Kaiserslautern Germany
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39
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McHugh TA, Compson Z, van Gestel N, Hayer M, Ballard L, Haverty M, Hines J, Irvine N, Krassner D, Lyons T, Musta EJ, Schiff M, Zint P, Schwartz E. Climate controls prokaryotic community composition in desert soils of the southwestern United States. FEMS Microbiol Ecol 2017; 93:4111145. [DOI: 10.1093/femsec/fix116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Theresa A. McHugh
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Zacchaeus Compson
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Canadian Rivers Institute, University of New Brunswick, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Natasja van Gestel
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Texas Tech University Climate Science Center, Lubbock, TX 79409, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
| | | | | | - Jeffrey Hines
- Northland Preparatory Academy, Flagstaff, AZ 86004, USA
| | - Nick Irvine
- Northland Preparatory Academy, Flagstaff, AZ 86004, USA
| | | | - Ted Lyons
- Coconino High School, Flagstaff, AZ 86004, USA
| | | | | | | | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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40
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Calderoli PA, Collavino MM, Behrends Kraemer F, Morrás HJM, Aguilar OM. Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of the N 2 -fixing community depending on depth and agricultural use of soil. Microbiologyopen 2017; 6. [PMID: 28766873 PMCID: PMC5635172 DOI: 10.1002/mbo3.502] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/20/2017] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
In this survey, a total of 80 787 reads and 28 171 unique NifH protein sequences were retrieved from soil RNA. This dataset extends our knowledge about the structure and diversity of the functional diazotrophic communities in agricultural soils from Argentinean Pampas. Operational taxonomic unit (OTU)‐based analyses showed that nifH phylotypes related to Geobacter and Anaeromyxobacter (44.8%), Rhizobiales (29%), Cyanobacteria (16.7%), and Verrucomicrobiales (8%) are key microbial components of N2 fixation in soils associated with no‐till management and soil depth. In addition, quantification of nifH gene copies related to Geobacter and Cyanobacteria revealed that these groups are abundant in soils under maize–soybean rotation and soybean monoculture, respectively. The correlation of physicochemical soil parameters with the diazotrophic diversity and composition showed that soil stability and organic carbon might contribute to the functional signatures of particular nifH phylotypes in fields under no‐till management. Because crop production relies on soil‐borne microorganism's activities, such as free N2 fixation, the information provided by our study on the diazotrophic population dynamics, associated with the edaphic properties and land‐use practices, represents a major contribution to gain insight into soil biology, in which functionally active components are identified.
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Affiliation(s)
- Priscila A Calderoli
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina
| | - Mónica M Collavino
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - Filipe Behrends Kraemer
- Cátedra de Manejo y Conservación de Suelos, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INTA-CIRN, Instituto de Suelos, Hurlingham, Provincia de Buenos Aires, Argentina
| | - Héctor J M Morrás
- INTA-CIRN, Instituto de Suelos, Hurlingham, Provincia de Buenos Aires, Argentina
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina
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41
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Bates ST, Nash TH, Garcia-Pichel F. Patterns of diversity for fungal assemblages of biological soil crusts from the southwestern United States. Mycologia 2017; 104:353-61. [PMID: 22123652 DOI: 10.3852/11-232] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Scott T. Bates
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309
| | - Thomas H. Nash
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, Arizona 85287-4501
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, P.O. Box 874501, Tempe, Arizona 85287-4501
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42
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Zeng J, Lou K, Zhang CJ, Wang JT, Hu HW, Shen JP, Zhang LM, Han LL, Zhang T, Lin Q, Chalk PM, He JZ. Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China. Front Microbiol 2016; 7:1353. [PMID: 27625641 PMCID: PMC5003921 DOI: 10.3389/fmicb.2016.01353] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 08/16/2016] [Indexed: 12/04/2022] Open
Abstract
Structural succession and its driving factors for nitrogen (N) cycling microbial communities during the early stages of soil development (0–44 years) were studied along a chronosequence in the glacial forelands of the Tianshan Mountain No.1 glacier in the arid and semi-arid region of central Asia. We assessed the abundance and population of functional genes affiliated with N-fixation (nifH), nitrification (bacterial and archaeal amoA), and denitrification (nirK/S and nosZ) in a glacier foreland using molecular methods. The abundance of functional genes significantly increased with soil development. N cycling community compositions were also significantly shifted within 44 years and were structured by successional age. Cyanobacterial nifH gene sequences were the most dominant N fixing bacteria and its relative abundance increased from 56.8–93.2% along the chronosequence. Ammonia-oxidizing communities shifted from the Nitrososphaera cluster (AOA-amoA) and the Nitrosospira cluster ME (AOB-aomA) in younger soils (0 and 5 years) to communities dominated by soil and sediment 1 (AOA-amoA) and Nitrosospira Cluster 2 Related (AOB-aomA) in older soils (≥17 years). Most of the denitrifers closest relatives were potential aerobic denitrifying bacteria, and some other types of denitrifying bacteria (like autotrophic nitrate-reducing, sulfide-oxidizing bacteria and denitrifying phosphorus removing bacteria) were also detected in all soil samples. The regression analysis showed that N cycling microbial communities were dominant in younger soils (0–5 years) and significantly correlated with soil total carbon, while communities that were most abundant in older soils were significantly correlated with soil total nitrogen. These results suggested that the shift of soil C and N contents during the glacial retreat significantly influenced the abundance, composition and diversity of N cycling microbial communities.
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Affiliation(s)
- Jun Zeng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China; Institute of Applied Microbiology, Xinjiang Academy of Agricultural SciencesUrumqi, China
| | - Kai Lou
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences Urumqi, China
| | - Cui-Jing Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne VIC, Australia
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Tao Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences Urumqi, China
| | - Qin Lin
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences Urumqi, China
| | - Phillip M Chalk
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, MelbourneVIC, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, MelbourneVIC, Australia
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Description of Deinococcus oregonensis sp. nov., from biological soil crusts in the Southwestern arid lands of the United States of America. Arch Microbiol 2016; 199:69-76. [PMID: 27515516 DOI: 10.1007/s00203-016-1273-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/21/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Abstract
Biological soil crusts are distinct habitats, harbor unique prokaryotic diversity and gave an impetus to isolate novel species. In the present study, a pink-pigmented bacterium, (OR316-6T), was isolated from biological soil crusts using oligotrophic BG11-PGY medium. Strain OR316-6T was Gram-positive, short rods, non-motile and non-spore forming. Cells were positive for catalase, oxidase and β-galactosidase and negative for most of the enzymatic activities. The major fatty acids present were C16:0, C17:0, and C16:1ω7c and contained MK-8 and MK-10 as the predominant menaquinones. The cell wall peptidoglycan was of A3β variant with L-ornithine as the diamino acid. Based on the above characteristics, strain OR316-6T was assigned to the genus Deinococcus. The phylogenetic analysis indicated that strain OR316-6T was closely related to D. aquatilis DSM 23025T with a 16S rRNA gene similarity of 99.3 % and clustered with a bootstrap value of 100 %. DNA-DNA similarity between strain OR316-6T and D. aquatilis DSM 23025T was 37.0 % indicating that strain OR316-6T was a novel species. Further, DNA fingerprinting of stains OR316-6T and D. aquatilis DSM 23035T demonstrated that both strains were related to each other with a similarity coefficient of only 0.32 and supported the species status to strain OR316-6T. In addition, phenotypic characteristics distinguished strain OR316-6T from D. aquatilis DSM 23025T. Based on the cumulative differences, strain OR316-16T exhibited with its closely related species, it was identified as a novel species and proposed the name Deinococcus oregonensis sp. nov. The type strain is D. oregonensis sp. nov. (OR316-6T = JCM 13503T = DSM 17762T).
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Wang P, Zhao S, Wang X, Zhang Y, Zheng N, Wang J. Ruminal Methanogen Community in Dairy Cows Fed Agricultural Residues of Corn Stover, Rapeseed, and Cottonseed Meals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5439-5445. [PMID: 27322573 DOI: 10.1021/acs.jafc.6b00708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The purpose was to reveal changes in the methanogen community in the rumen of dairy cows fed agricultural residues of corn stover, rapeseed, and cottonseed meals, compared with alfalfa hay or soybean meal. Analysis was based on cloning and sequencing the methyl coenzyme M reductase α-subunit gene of ruminal methanogens. Results revealed that predicted methane production was increased while population of ruminal methanogens was not significantly affected when cows were fed diets containing various amounts of agricultural residues. Richness and diversity of methanogen community were markedly increased by addition of agricultural residues. The dominant ruminal methanogens shared by all experimental groups belonged to rumen cluster C, accounting for 71% of total, followed by the order Methanobacteriales (29%). Alterations of ruminal methanogen community and prevalence of particular species occurred in response to fed agricultural residue rations, suggesting the possibility of regulating target methanogens to control methane production by dairy cows fed agricultural residues.
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Affiliation(s)
- Pengpeng Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Xingwen Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Laboratory of Quality & Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences , Beijing 100193, People's Republic of China
- Milk and Dairy Production Inspection Center of Ministry of Agriculture (Beijing) , Beijing, 100193, People's Republic of China
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Williams L, Loewen-Schneider K, Maier S, Büdel B. Cyanobacterial diversity of western European biological soil crusts along a latitudinal gradient. FEMS Microbiol Ecol 2016; 92:fiw157. [PMID: 27411981 PMCID: PMC4970567 DOI: 10.1093/femsec/fiw157] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2016] [Indexed: 01/26/2023] Open
Abstract
Cyanobacteria associated with biological soil crusts (BSCs) have important attributes, such as nitrogen fixation and soil stabilisation. However, research on these organisms has been minimal, and their diversity and distribution throughout temperate Europe is currently unknown. The SCIN (Soil Crust International) project is a multidisciplinary research initiative that aims to achieve improved understanding of the BSCs of Europe, one facet being an investigation into the cyanobacterial communities of BSCs across a latitudinal gradient. Cyanobacteria assemblages were analysed by both morphological and molecular analysis. Two treatments were applied prior to DNA extraction, continued sample wetting and a dry sample process, and 16S ribosomal RNA (rRNA) amplicons were processed by Illumina MiSeq sequencing. The results reveal high and variable cyanobacterial diversity with each site showing a unique assemblage. Many common cyanobacterial genera, for example Nostoc and Microcoleus, were found in all sites but the abundances of different genera varied considerably. The polyphasic approach was found to be essential in recording the presence of important cyanobacteria that a single method itself did not highlight. The wet and dry treatments showed some differences in diversity, but mainly in abundance, this may suggest how cyanobacterial composition of BSCs changes with seasonal variability. Investigating the diversity and community composition of cyanobacteria associated with biological soil crusts in climatically different regions of Europe.
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Affiliation(s)
- Laura Williams
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, PO Box 3049, 67653 Kaiserslautern, Germany
| | - Katharina Loewen-Schneider
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, PO Box 3049, 67653 Kaiserslautern, Germany
| | - Stefanie Maier
- Institute of Plant Sciences, University of Graz, 8010 Graz, Austria
| | - Burkhard Büdel
- Plant Ecology and Systematics, Biology Institute, University of Kaiserslautern, PO Box 3049, 67653 Kaiserslautern, Germany
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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47
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Bio-electrochemical conversion of atmospheric N2 to ammonium using free-living diazotrophs. KOREAN J CHEM ENG 2016. [DOI: 10.1007/s11814-016-0011-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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48
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Zhang B, Kong W, Wu N, Zhang Y. Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China. J Basic Microbiol 2016; 56:670-9. [PMID: 26947139 DOI: 10.1002/jobm.201500751] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/06/2016] [Indexed: 11/11/2022]
Abstract
Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as Sphingomonas sp. Niastella sp., Pedobacter, and Candidatus solobacter increased. Therefore, bacterial community composition and their key ecological roles shifted to the development of BSCs.
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Affiliation(s)
- Bingchang Zhang
- Key Laboratory of Biogeography and Bioresources in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Nan Wu
- Key Laboratory of Biogeography and Bioresources in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yuanming Zhang
- Key Laboratory of Biogeography and Bioresources in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
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Pushkareva E, Johansen JR, Elster J. A review of the ecology, ecophysiology and biodiversity of microalgae in Arctic soil crusts. Polar Biol 2016. [DOI: 10.1007/s00300-016-1902-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Pepe-Ranney C, Koechli C, Potrafka R, Andam C, Eggleston E, Garcia-Pichel F, Buckley DH. Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation. THE ISME JOURNAL 2016; 10:287-98. [PMID: 26114889 PMCID: PMC4737922 DOI: 10.1038/ismej.2015.106] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 11/08/2022]
Abstract
Biological soil crusts (BSCs) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface. In particular, BSC N2-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems. In mature crusts, N2-fixation is largely attributed to heterocystous cyanobacteria; however, early successional crusts possess few N2-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development. DNA stable isotope probing with (15)N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate (15)N2 in early successional crusts. The Clostridiaceae identified are divergent from previously characterized isolates, though N2-fixation has previously been observed in this family. The Proteobacteria identified share >98.5% small subunit rRNA gene sequence identity with isolates from genera known to possess diazotrophs (for example, Pseudomonas, Klebsiella, Shigella and Ideonella). The low abundance of these heterotrophic diazotrophs in BSCs may explain why they have not been characterized previously. Diazotrophs have a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSCs in arid ecosystems.
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Affiliation(s)
- Charles Pepe-Ranney
- Department of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Chantal Koechli
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Ruth Potrafka
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Cheryl Andam
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Erin Eggleston
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Daniel H Buckley
- Department of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
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