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Lu J, Wang J, Zhang J, Zhu Y, Qin L, Zhu B. Diversity of Culturable Endophytic Fungi in Crocus sativus and Their Correlation with Crocin Content. Curr Microbiol 2023; 80:73. [PMID: 36622432 DOI: 10.1007/s00284-023-03177-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023]
Abstract
The presence and diversity of endophytic fungi associated with host plants are important not just for host plant growth and defense, but also impact the production of medicinal secondary metabolites. However, the correlation between endophytic fungi and crocin production in Crocus sativus (CS) remains underexplored. Here, we explore the relationship between endophytic fungal diversity and crocin content among different CS tissues and field sites. Specifically, we isolated endophytic fungi from five different field sites (Shanghai, Jiande, Huzhou, Anhui, and Hebei) and five different tissues (corm, scape, leaf, petal, and stigma) and analyzed fungal community diversity, richness, and evenness. We identified a total of 32 endophytic fungal taxa, assigned to 7 orders within 4 classes (Eurotiomycetes, Agaricomycetes, Dothideomycetes, and Sordariomycetes). The most dominant order was Eurotiales, and the most dominant genera were Penicillium and Talaromyces. Species richness tended to be highest in belowgrown tissues, such as corm and scape. Additionally, several fungal taxa were found to be either site- or tissue-specific. Three genera in particular were correlated with crocin content: Penicillium, Sistotrema, and Bjerkandera. Given the fact that endophytic microorganisms can both promote the production of secondary metabolites in host plants and potentially produce secondary metabolites themselves, further study is required to understand the mechanistic relationship between these and other fungal genera and crocin production.
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Affiliation(s)
- Jiemiao Lu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jie Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiahao Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yichun Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Lupin Qin
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Bo Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China.
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2
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Son D, Lee EJ. Soil Microbial Communities Associated with Three Arctic Plants in Different Local Environments in Ny-Ålesund, Svalbard. J Microbiol Biotechnol 2022; 32:1275-1283. [PMID: 36198667 PMCID: PMC9668094 DOI: 10.4014/jmb.2208.08009] [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: 08/08/2022] [Revised: 09/02/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022]
Abstract
Understanding soil microbial community structure in the Arctic is essential for predicting the impact of climate change on interactions between organisms living in polar environments. The hypothesis of the present study was that soil microbial communities and soil chemical characteristics would vary depending on their associated plant species and local environments in Arctic mature soils. We analyzed soil bacterial communities and soil chemical characteristics from soil without vegetation (bare soil) and rhizosphere soil of three Arctic plants (Cassiope tetragona [L.] D. Don, Dryas octopetala L. and Silene acaulis [L.] Jacq.) in different local environments (coal-mined site and seashore-adjacent site). We did not observe any clear differences in microbial community structure in samples belonging to different plant rhizospheres; however, samples from different environmental sites had distinct microbial community structure. The samples from coal-mined site had a relatively higher abundance of Bacteroidetes and Firmicutes. On the other hand, Acidobacteria was more prevalent in seashore-adjacent samples. The relative abundance of Proteobacteria and Acidobacteria decreased toward higher soil pH, whereas that of Bacteroidetes and Firmicutes was positively correlated with soil pH. Our results suggest that soil bacterial community dissimilarity can be driven by spatial heterogeneity in deglaciated mature soil. Furthermore, these results indicate that soil microbial composition and relative abundance are more affected by soil pH, an abiotic factor, than plant species, a biotic factor.
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Affiliation(s)
- Deokjoo Son
- College of Education Department of Science Education, Dankook University, Gyeonggi-do 16890, Republic of Korea,Corresponding author Phone: +82-31-8005-3844 E-mail:
| | - Eun Ju Lee
- Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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3
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Jackson AC, Jorna J, Chaston JM, Adams BJ. Glacial Legacies: Microbial Communities of Antarctic Refugia. BIOLOGY 2022; 11:biology11101440. [PMID: 36290344 PMCID: PMC9598129 DOI: 10.3390/biology11101440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
In the cold deserts of the McMurdo Dry Valleys (MDV) the suitability of soil for microbial life is determined by both contemporary processes and legacy effects. Climatic changes and accompanying glacial activity have caused local extinctions and lasting geochemical changes to parts of these soil ecosystems over several million years, while areas of refugia may have escaped these disturbances and existed under relatively stable conditions. This study describes the impact of historical glacial and lacustrine disturbance events on microbial communities across the MDV to investigate how this divergent disturbance history influenced the structuring of microbial communities across this otherwise very stable ecosystem. Soil bacterial communities from 17 sites representing either putative refugia or sites disturbed during the Last Glacial Maximum (LGM) (22-17 kya) were characterized using 16 S metabarcoding. Regardless of geographic distance, several putative refugia sites at elevations above 600 m displayed highly similar microbial communities. At a regional scale, community composition was found to be influenced by elevation and geographic proximity more so than soil geochemical properties. These results suggest that despite the extreme conditions, diverse microbial communities exist in these putative refugia that have presumably remained undisturbed at least through the LGM. We suggest that similarities in microbial communities can be interpreted as evidence for historical climate legacies on an ecosystem-wide scale.
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Affiliation(s)
- Abigail C. Jackson
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (A.C.J.); (J.J.)
| | - Jesse Jorna
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (A.C.J.); (J.J.)
| | - John M. Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Byron J. Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
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4
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Doytchinov VV, Dimov SG. Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060916. [PMID: 35743947 PMCID: PMC9228076 DOI: 10.3390/life12060916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.
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Jiang X, Van Horn DJ, Okie JG, Buelow HN, Schwartz E, Colman DR, Feeser KL, Takacs-Vesbach CD. Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient. Extremophiles 2022; 26:15. [PMID: 35296937 DOI: 10.1007/s00792-022-01262-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.
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Affiliation(s)
- Xiaoben Jiang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - David J Van Horn
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Heather N Buelow
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Daniel R Colman
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kelli L Feeser
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Wang DD, Zhao W, Reyila M, Huang KC, Liu S, Cui BK. Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale. Microorganisms 2022; 10:microorganisms10020371. [PMID: 35208826 PMCID: PMC8877128 DOI: 10.3390/microorganisms10020371] [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: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/03/2022] [Indexed: 02/06/2023] Open
Abstract
Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand.
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Affiliation(s)
| | | | | | | | | | - Bao-Kai Cui
- Correspondence: ; Tel./Fax: +86-10-6233-6309
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7
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Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils. mSystems 2022; 7:e0133021. [PMID: 35040702 PMCID: PMC8765064 DOI: 10.1128/msystems.01330-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.
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8
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Herrero J, Puigserver D, Nijenhuis I, Kuntze K, Carmona JM. Key factors controlling microbial distribution on a DNAPL source area. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1508-1520. [PMID: 34355320 PMCID: PMC8724114 DOI: 10.1007/s11356-021-15635-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/21/2021] [Indexed: 05/03/2023]
Abstract
Chlorinated solvents are among the common groundwater contaminants that show high complexity in their distribution in the subsoil. Microorganisms play a vital role in the natural attenuation of chlorinated solvents. Thus far, how the in situ soil microbial community responds to chlorinated solvent contamination has remained unclear. In this study, the microbial community distribution within two boreholes located in the source area of perchloroethene (PCE) was investigated via terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis. Microbial data were related to the lithological and geochemical data and the concentration and isotopic composition of chloroethenes to determine the key factors controlling the distribution of the microbial communities. The results indicated that Proteobacteria, Actinobacteria, and Firmicutes were the most abundant phylums in the sediment. The statistical correlation with the environmental data proved that fine granulometry, oxygen tolerance, terminal electron-acceptor processes, and toxicity control microbial structure. This study improves our understanding of how the microbial community in the subsoil responds to high concentrations of chlorinated solvents.
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Affiliation(s)
- Jofre Herrero
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, The Water Research Institute (IdRA), University of Barcelona, C/ Martí Franquès sn, Barcelona, Spain.
| | - Diana Puigserver
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, The Water Research Institute (IdRA), University of Barcelona, C/ Martí Franquès sn, Barcelona, Spain
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry (ISOBIO), UFZ Centre for Environmental Research Leipzig-Halle, Permoserstr. 15, 04318, Leipzig, Germany
| | - Kevin Kuntze
- Department of Isotope Biogeochemistry (ISOBIO), UFZ Centre for Environmental Research Leipzig-Halle, Permoserstr. 15, 04318, Leipzig, Germany
- Isodetect, Deutscher Platz 5b, 04103, Leipzig, Germany
| | - José M Carmona
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, The Water Research Institute (IdRA), University of Barcelona, C/ Martí Franquès sn, Barcelona, Spain
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9
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康 巍. Research Progress on the Effects of Nitrogen Addition on Soil and Rhizosphere Microbial Community Structure. INTERNATIONAL JOURNAL OF ECOLOGY 2022. [DOI: 10.12677/ije.2022.112023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Zhang L, Delgado-Baquerizo M, Shi Y, Liu X, Yang Y, Chu H. Co-existing water and sediment bacteria are driven by contrasting environmental factors across glacier-fed aquatic systems. WATER RESEARCH 2021; 198:117139. [PMID: 33895591 DOI: 10.1016/j.watres.2021.117139] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/25/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Glacier-fed aquatic ecosystems provide habitats for diverse and active bacterial communities. However, the environmental vulnerabilities of co-existing water and sediment bacterial communities in these ecosystems remain unclear. Here, 16S rRNA gene sequencing was used to investigate co-existing bacterial communities in paired water and sediment samples from multiple rivers and lakes that are mainly fed by glaciers from the southeast Tibetan Plateau. Overall, the bacterial communities were dissimilar between the water and sediment, which indicated that there were limited interactions between them. Bacterial diversity was greatest in the sediments, where it was mainly driven by changes in nitrogen compounds and pH. Meanwhile water bacterial diversity was more susceptible to evapotranspiration, elevation, and mean annual temperature. Water samples contained higher proportions of Proteobacteria and Bacteroidetes, while sediment harbored higher proportions of Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Cyanobacteria, and Gemmatimonadetes. Bacterial community composition was significantly correlated with mean annual precipitation in water, but with nitrogen compounds in sediment. The co-occurrence network of water included more keystone species (e.g., CL500-29 marine group, Nocardioides spp., and Bacillus spp.) than the sediment network. These keystone species showed stronger phylogenetic signals than the species in the modular structures. Further, ecological clusters within the networks suggested that there were contrasting environmental vulnerabilities and preferences between water and sediment communities. These findings demonstrated that co-existing water and sediment bacterial communities and ecological clusters were shaped by contrasting environmental factors. This work provides a basis for understanding the importance of bacterial communities in maintaining glacier-fed aquatic ecosystems. Further, the results provide new perspectives for water resource management and water conservation in changing environments.
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Affiliation(s)
- Liyan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China.
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Sansupa C, Purahong W, Wubet T, Tiansawat P, Pathom-Aree W, Teaumroong N, Chantawannakul P, Buscot F, Elliott S, Disayathanoowat T. Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand. PLoS One 2021; 16:e0248806. [PMID: 33831034 PMCID: PMC8031335 DOI: 10.1371/journal.pone.0248806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/07/2021] [Indexed: 11/19/2022] Open
Abstract
Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.
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Affiliation(s)
- Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Graduate School, Chiang Mai University, Chiang Mai, Thailand
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- * E-mail: (TD); (WP)
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Pimonrat Tiansawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Environmental Science Research Centre and Forest Restoration Research Unit, Biology Department, Science Faculty, Chiang Mai University, Chiang Mai, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | | | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Stephen Elliott
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Environmental Science Research Centre and Forest Restoration Research Unit, Biology Department, Science Faculty, Chiang Mai University, Chiang Mai, Thailand
| | - Terd Disayathanoowat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- * E-mail: (TD); (WP)
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12
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Rawat M, Arunachalam K, Arunachalam A. Seasonal dynamics in soil microbial biomass C, N and P in a temperate forest ecosystem of Uttarakhand, India. Trop Ecol 2021. [DOI: 10.1007/s42965-021-00153-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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13
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George SF, Fierer N, Levy JS, Adams B. Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity. Front Microbiol 2021; 12:616730. [PMID: 33584618 PMCID: PMC7873294 DOI: 10.3389/fmicb.2021.616730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.
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Affiliation(s)
- Scott F George
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
| | - Joseph S Levy
- Department of Geology, Colgate University, Hamilton, NY, United States
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, United States.,Monte L. Bean Museum, Brigham Young University, Provo, UT, United States
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14
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Zhang W, Bahadur A, Sajjad W, Zhang G, Nasir F, Zhang B, Wu X, Liu G, Chen T. Bacterial Diversity and Community Composition Distribution in Cold-Desert Habitats of Qinghai-Tibet Plateau, China. Microorganisms 2021; 9:microorganisms9020262. [PMID: 33514038 PMCID: PMC7911287 DOI: 10.3390/microorganisms9020262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
Bacterial communities in cold-desert habitats play an important ecological role. However, the variation in bacterial diversity and community composition of the cold-desert ecosystem in Qinghai–Tibet Plateau remains unknown. To fill this scientific gape, Illumina MiSeq sequencing was performed on 15 soil samples collected from different cold-desert habitats, including human-disturbed, vegetation coverage, desert land, and sand dune. The abundance-based coverage estimator, Shannon, and Chao indices showed that the bacterial diversity and abundance of the cold-desert were high. A significant variation reported in the bacterial diversity and community composition across the study area. Proteobacteria accounted for the largest proportion (12.4–55.7%) of all sequences, followed by Actinobacteria (9.2–39.7%), Bacteroidetes (1.8–21.5%), and Chloroflexi (2.7–12.6%). Furthermore, unclassified genera dominated in human-disturbed habitats. The community profiles of GeErMu, HongLiangHe, and CuoNaHu sites were different and metagenomic biomarkers were higher (22) in CuoNaHu sites. Among the soil physicochemical variables, the total nitrogen and electric conductivity significantly influenced the bacterial community structure. In conclusion, this study provides information regarding variation in diversity and composition of bacterial communities and elucidates the association between bacterial community structures and soil physicochemical variables in cold-desert habitats of Qinghai–Tibet Plateau.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (W.Z.); (G.Z.); (X.W.)
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; (A.B.); (B.Z.)
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; (A.B.); (B.Z.)
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China;
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China;
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (W.Z.); (G.Z.); (X.W.)
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; (A.B.); (B.Z.)
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China;
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; (A.B.); (B.Z.)
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China;
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (W.Z.); (G.Z.); (X.W.)
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; (A.B.); (B.Z.)
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; (W.Z.); (G.Z.); (X.W.)
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; (A.B.); (B.Z.)
- Correspondence: (G.L.); (T.C.); Tel.: +86-0931-8273670 (T.C.)
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China;
- Correspondence: (G.L.); (T.C.); Tel.: +86-0931-8273670 (T.C.)
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15
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Zhou Z, Yu M, Ding G, Gao G, He Y. Diversity and structural differences of bacterial microbial communities in rhizocompartments of desert leguminous plants. PLoS One 2020; 15:e0241057. [PMID: 33351824 PMCID: PMC7755220 DOI: 10.1371/journal.pone.0241057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
By assessing diversity variations of bacterial communities under different rhizocompartment types (i.e., roots, rhizosphere soil, root zone soil, and inter-shrub bulk soil), we explore the structural difference of bacterial communities in different root microenvironments under desert leguminous plant shrubs. Results will enable the influence of niche differentiation of plant roots and root soil on the structural stability of bacterial communities under three desert leguminous plant shrubs to be examined. High-throughput 16S rRNA genome sequencing was used to characterize diversity and structural differences of bacterial microbes in the rhizocompartments of three xeric leguminous plants. Results from this study confirm previous findings relating to niche differentiation in rhizocompartments under related shrubs, and they demonstrate that diversity and structural composition of bacterial communities have significant hierarchical differences across four rhizocompartment types under leguminous plant shrubs. Desert leguminous plants showed significant hierarchical filtration and enrichment of the specific bacterial microbiome across different rhizocompartments (P < 0.05). The dominant bacterial microbiome responsible for the differences in microbial community structure and composition across different niches of desert leguminous plants mainly consisted of Proteobacteria, Actinobacteria, and Bacteroidetes. All soil factors of rhizosphere and root zone soils, except for NO3-N and TP under C. microphylla and the two Hedysarum spp., recorded significant differences (P < 0.05). Moreover, soil physicochemical factors have a significant impact on driving the differentiation of bacterial communities under desert leguminous plant shrubs. By investigating the influence of niches on the structural difference of soil bacterial communities with the differentiation of rhizocompartments under desert leguminous plant shrubs, we provide data support for the identification of dominant bacteria and future preparation of inocula, and provide a foundation for further study of the host plants-microbial interactions.
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Affiliation(s)
- Ziyuan Zhou
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Minghan Yu
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- * E-mail: (MY); (GD)
| | - Guodong Ding
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- * E-mail: (MY); (GD)
| | - Guanglei Gao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Yingying He
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
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16
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Li Y, Chen J, Wang Y, Ma D, Rui W. The effects of the recombinant YeaZ of Vibrio harveyi on the resuscitation and growth of soil bacteria in extreme soil environment. PeerJ 2020; 8:e10342. [PMID: 33391864 PMCID: PMC7759134 DOI: 10.7717/peerj.10342] [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: 01/15/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022] Open
Abstract
Numerous bacteria entered the viable but non-culturable state due to the stresses of dry and salt in soils. YeaZ of Gram-negative bacteria is a resuscitation promoting factor (Rpf) homologous protein could resuscitate bacteria of natural environment in VBNC state. To investigate the promoting effect of YeaZ on the isolation of viable but non-culturable (VBNC) bacteria from soil samples in extreme environments, the recombinant YeaZ of Vibrio harveyi was prepared and added to the soil samples from volcanic soil and saline soil in Northwest China. The study has shown that YeaZ can promote the recovery and growth of soil microorganisms, and the number of cultivable bacteria in volcanic and saline soil has increased from 0.17 × 103 and 2.03 × 103 cfu⋅ml−1 to 1.00 × 103 and 5.55 × 103 cfu⋅ml−1, respectively. The 16S rDNA gene sequencing and phylogenetic analysis showed that YeaZ played an essential role in the increase of composition and diversity of bacteria. A total of 13 bacterial strains were isolated from the volcanic soil samples, which belong to phyla Actinobacteria, Firmicutes and Gamma-proteobacteria. Four species, including Ornithinimicrobium kibberense, Agrococcus citreus, Stenotrophomonas rhizophila and Pseudomonas zhaodongensis were found in the control group, while Micrococcus antarcticus, Kocuria rose, Salinibacterium xinjiangense, Planococcus antarcticus, Ornithinimicrobium kibberense and Pseudomonas zhaodongensis were isolated from the treatment groups (addition of YeaZ). Twenty-one strains were isolated from the saline soil samples, including eight species from the control group and thirteen species from the treatment groups, among which nine species were only found, including Bacillus oceanisediminis, Brevibacillus brevis, Paenibacillus xylanilyticus, Microbacterium maritypicum, B. subtilis, B. alcalophilus, B. niabensis, Oceanimonas doudoroffii and Zobellella taiwanensis. The results suggest that addition of YeaZ to soil samples can promote the recovery of VBNC. This method has the implications for the discovery of VBNC bacteria that have potential environmental functions.
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Affiliation(s)
- Yanlin Li
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China.,Chongqing Key Laboratory of Environmental Materials & Remediation Technologies/College of Chemistry and Environmental Engineering, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Yonggang Wang
- School of life science and engineering, Lanzhou University of Technology, Lanzhou, China
| | - Dan Ma
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Wenhong Rui
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
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17
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Bottos EM, Laughlin DC, Herbold CW, Lee CK, McDonald IR, Cary SC. Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica. FEMS Microbiol Ecol 2020; 96:5815075. [PMID: 32239205 DOI: 10.1093/femsec/fiaa042] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.
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Affiliation(s)
- Eric M Bottos
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Daniel C Laughlin
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Craig W Herbold
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Charles K Lee
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Ian R McDonald
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - S Craig Cary
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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18
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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19
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Zhang W, Bahadur A, Zhang G, Zhang B, Wu X, Chen T, Liu G. Diverse Bacterial Communities From Qaidam Basin of the Qinghai-Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions. Front Microbiol 2020; 11:554105. [PMID: 33042062 PMCID: PMC7530167 DOI: 10.3389/fmicb.2020.554105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
The Qaidam Basin of the Qinghai–Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The α-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general, Firmicutes was dominant in the west region, while Proteobacteria and Acidobacteria were dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
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20
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Vimercati L, Bueno de Mesquita CP, Schmidt SK. Limited Response of Indigenous Microbes to Water and Nutrient Pulses in High-Elevation Atacama Soils: Implications for the Cold-Dry Limits of Life on Earth. Microorganisms 2020; 8:E1061. [PMID: 32708721 PMCID: PMC7409055 DOI: 10.3390/microorganisms8071061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
Soils on the world's highest volcanoes in the Atacama region represent some of the harshest ecosystems yet discovered on Earth. Life in these environments must cope with high UV flux, extreme diurnal freeze-thaw cycles, low atmospheric pressure and extremely low nutrient and water availability. Only a limited spectrum of bacterial and fungal lineages seems to have overcome the harshness of this environment and may have evolved the ability to function in situ. However, these communities may lay dormant for most of the time and spring to life only when enough water and nutrients become available during occasional snowfalls and aeolian depositions. We applied water and nutrients to high-elevation soils (5100 meters above sea level) from Volcán Llullaillaco, both in lab microcosms and in the field, to investigate how microbial communities respond when resource limitations are alleviated. The dominant taxon in these soils, the extremophilic yeast Naganishia sp., increased in relative sequence abundance and colony-forming unit counts after water + nutrient additions in microcosms, and marginally in the field after only 6 days. Among bacteria, only a Noviherbaspirillum sp. (Oxalobacteraceae) significantly increased in relative abundance both in the lab and field in response to water addition but not in response to water and nutrients together, indicating that it might be an oligotroph uniquely suited to this extreme environment. The community structure of both bacteria and eukaryotes changed significantly with water and water + nutrient additions in the microcosms and taxonomic richness declined with amendments to water and nutrients. These results indicate that only a fraction of the detected community is able to become active when water and nutrients limitations are alleviated in lab microcosms, and that water alone can dramatically change community structure. Our study sheds light on which extremophilic organisms are likely to respond when favorable conditions occur in extreme earthly environments and perhaps in extraterrestrial environments as well.
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Affiliation(s)
- Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA; (L.V.); (C.P.B.d.M.)
| | - Clifton P. Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA; (L.V.); (C.P.B.d.M.)
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309-0450, USA
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA; (L.V.); (C.P.B.d.M.)
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21
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Niederberger TD, Bottos EM, Sohm JA, Gunderson T, Parker A, Coyne KJ, Capone DG, Carpenter EJ, Cary SC. Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils. Front Microbiol 2019; 10:621. [PMID: 31019494 PMCID: PMC6458288 DOI: 10.3389/fmicb.2019.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
The cold deserts of the McMurdo Dry Valleys (MDV), Antarctica, host a high level of microbial diversity. Microbial composition and biomass in arid vs. ephemerally wetted regions are distinctly different, with wetted communities representing hot spots of microbial activity that are important zones for biogeochemical cycling. While climatic change is likely to cause wetting in areas not historically subject to wetting events, the responses of microorganisms inhabiting arid soils to water addition is unknown. The purpose of this study was to observe how an associated, yet non-wetted microbial community responds to an extended addition of water. Water from a stream was diverted to an adjacent area of arid soil with changes in microbial composition and activities monitored via molecular and biochemical methods over 7 weeks. The frequency of genetic signatures related to both prokaryotic and eukaryotic organisms adapted to MDV aquatic conditions increased during the limited 7 week period, indicating that the soil community was transitioning into a typical "high-productivity" MDV community. This work is consistent with current predictions that MDV microbial communities in arid regions are highly sensitive to climate change, and further supports the notion that changes in community structure and associated biogeochemical cycling may occur much more rapidly than predicted.
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Affiliation(s)
- Thomas D Niederberger
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Eric M Bottos
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand.,Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jill A Sohm
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Troy Gunderson
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Alex Parker
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Kathryn J Coyne
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Douglas G Capone
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Edward J Carpenter
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Stephen Craig Cary
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand
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22
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Plassart P, Prévost-Bouré NC, Uroz S, Dequiedt S, Stone D, Creamer R, Griffiths RI, Bailey MJ, Ranjard L, Lemanceau P. Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect. Sci Rep 2019; 9:605. [PMID: 30679566 PMCID: PMC6345909 DOI: 10.1038/s41598-018-36867-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/14/2018] [Indexed: 11/09/2022] Open
Abstract
To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.
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Affiliation(s)
- Pierre Plassart
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | | | - Stéphane Uroz
- UMR 1136 Interactions Arbres Micro-organismes, INRA Univ Lorraine, F-54280, Champenoux, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | | | - Rachel Creamer
- TEAGASC, Johnstown Castle, Wexford, Ireland.,Wageningen University and Research, Wageningen, The Netherlands
| | - Robert I Griffiths
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - Mark J Bailey
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, UK
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
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23
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Evaluating the diversity and composition of bacterial communities associated with Vachellia pachyceras - the only existing native tree species in the Kuwait desert. Can J Microbiol 2018; 65:235-251. [PMID: 30495976 DOI: 10.1139/cjm-2018-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We investigated the diversity and composition of bacterial communities in rhizospheric and non-rhizospheric bulk soils as well as root nodule bacterial communities of Vachellia pachyceras - the only native tree species existing in the Kuwait desert. Community fingerprinting comparisons and 16S rDNA sequence identifications were used for characterization of the bacterial population using specific primers. The bacterial characterization of soil samples revealed four major phyla: Acidobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. In situ (desert) samples of both rhizospheric and non-rhizospheric bulk soil were dominated by the bacterial phyla Firmicutes and Bacteroidetes, whereas the phylum Betaproteobacteria was present only in non-rhizospheric bulk soil. Ex situ (nursery growing condition) V. pachyceras resulted in restricted bacterial communities dominated by members of a single phylum, Bacteroidetes. Results indicated that the soil organic matter and rhizospheric environments might drive the bacterial community. Despite harsh climatic conditions, data demonstrated that V. pachyceras roots harbor endophytic bacterial populations. Our findings on bacterial community composition and structure have major significance for evaluating how Kuwait's extreme climatic conditions affect bacterial communities. The baseline data obtained in this study will be useful and assist in formulating strategies in ecological restoration programs, including the application of inoculation technologies.
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Affiliation(s)
- Majda K Suleiman
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Kingsley Dixon
- b Department of Environment and Agriculture, ARC Centre for Mine Site Restoration Curtin University, Bentley, WA 6102, Australia
| | - Lucy Commander
- c School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Paul Nevill
- d Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Ali M Quoreshi
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Narayana R Bhat
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Anitha J Manuvel
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
| | - Mini T Sivadasan
- a Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, P.O. Box 24885, Safat 13109, Kuwait
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Feeser KL, Van Horn DJ, Buelow HN, Colman DR, McHugh TA, Okie JG, Schwartz E, Takacs-Vesbach CD. Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert. Front Microbiol 2018; 9:1928. [PMID: 30186257 PMCID: PMC6110917 DOI: 10.3389/fmicb.2018.01928] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023] Open
Abstract
The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal-Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus-Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.
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Affiliation(s)
- Kelli L. Feeser
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - David J. Van Horn
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Heather N. Buelow
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Daniel R. Colman
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Theresa A. McHugh
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, United States
| | - Jordan G. Okie
- School of Life Sciences, School of Earth and Space Exploration, Arizona State University, Tempe, AZ, United States
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
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Solon AJ, Vimercati L, Darcy JL, Arán P, Porazinska D, Dorador C, Farías ME, Schmidt SK. Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone. MICROBIAL ECOLOGY 2018; 76:340-351. [PMID: 29305629 DOI: 10.1007/s00248-017-1129-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.
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Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - J L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - C Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - M E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, PROIMI, Tucumán, Argentina
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
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Lan G, Li Y, Lesueur D, Wu Z, Xie G. Seasonal changes impact soil bacterial communities in a rubber plantation on Hainan Island, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:826-834. [PMID: 29396343 DOI: 10.1016/j.scitotenv.2018.01.147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Rubber plantations have expanded rapidly over the past 20 years in tropical Asia and their impacts on regional ecosystems have garnered much concern. While much attention has been given to the negative impacts on aboveground diversity and function, the belowground bacterial soil community has received much less attention. Here, we investigated the community composition and diversity of soil bacteria of rubber plantations on Hainan Island in south China. The goals of the study were to describe changes in bacterial compositions and diversity across seasons. We found that seasonality defined by differences in rainfall amount strongly influenced bacterial communities. At both the Phylum and Family levels, we found significant differences in the total number of taxa, as well as the composition of the community as a function of season. Diversity of soil samples in the dry-rainy season was highest of three seasons, suggesting that bacterial structure was more sensitive in alternate periods of season. Diversity in the rainy season was substantial lower than in dry season. Results from a redundancy analysis showed that seasonal changes explained the largest part (31.9%) of the total variance of bacterial community composition. In conclusion, seasonal change had the greatest influence on bacterial communities, which overshadowed the effects of soil nutrient as well as other factors, and controls the bacterial communities in soils of RP in tropical region of Hainan.
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Affiliation(s)
- Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou City, Hainan Province 571737, PR China; Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, PR China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou City, Hainan Province 571737, PR China.
| | - Yuwu Li
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, PR China.
| | - Didier Lesueur
- Eco & Sols, University Montpellier, CIRAD, Montpellier, France; CIRAD, UMR ECO & SOLS, CIAT-Asia, Hanoi, Vietnam; Deakin University, Melbourne, Australia
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou City, Hainan Province 571737, PR China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou City, Hainan Province 571737, PR China
| | - Guishui Xie
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou City, Hainan Province 571737, PR China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou City, Hainan Province 571737, PR China
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27
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Bell-Dereske L, Takacs-Vesbach C, Kivlin SN, Emery SM, Rudgers JA. Leaf endophytic fungus interacts with precipitation to alter belowground microbial communities in primary successional dunes. FEMS Microbiol Ecol 2017; 93:3071445. [PMID: 28334408 PMCID: PMC5827620 DOI: 10.1093/femsec/fix036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/10/2017] [Indexed: 11/13/2022] Open
Abstract
Understanding interactions between above- and belowground components of ecosystems is an important next step in community ecology. These interactions may be fundamental to predicting ecological responses to global change because indirect effects occurring through altered species interactions can outweigh or interact with the direct effects of environmental drivers. In a multiyear field experiment (2010-2015), we tested how experimental addition of a mutualistic leaf endophyte (Epichloë amarillans) associated with American beachgrass (Ammophila breviligulata) interacted with an altered precipitation regime (±30%) to affect the belowground microbial community. Epichloë addition increased host root biomass at the plot scale, but reduced the length of extraradical arbuscular mycorrhizal (AM) fungal hyphae in the soil. Under ambient precipitation alone, the addition of Epichloë increased root biomass per aboveground tiller and reduced the diversity of AM fungi in A. breviligulata roots. Furthermore, with Epichloë added, the diversity of root-associated bacteria declined with higher soil moisture, whereas in its absence, bacterial diversity increased with higher soil moisture. Thus, the aboveground fungal mutualist not only altered the abundance and composition of belowground microbial communities but also affected how belowground communities responded to climate, suggesting that aboveground microbes have potential for cascading influences on community dynamics and ecosystem processes that occur belowground.
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Affiliation(s)
- Lukas Bell-Dereske
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Stephanie N. Kivlin
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Sarah M. Emery
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Jennifer A. Rudgers
- Department of Biology, 1 University of New Mexico, Albuquerque, NM 87131, USA
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28
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Chen XW, Wong JTF, Leung AOW, Ng CWW, Wong MH. Comparison of plant and bacterial communities between a subtropical landfill topsoil 15years after restoration and a natural area. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 63:49-57. [PMID: 27561244 DOI: 10.1016/j.wasman.2016.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/14/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
Engineered sanitary landfills are becoming more and more common worldwide. Ecosystem restoration of capped sanitary landfills is essential to restore the disturbed environment. Comparing plant communities, as well as bacterial communities, in landfills and natural areas, offers an efficient way to assess the restoration status. However, such studies on the restored engineered landfills are limited. Here we present an ecological restoration case in an engineered landfill in a subtropical region. Part of the South East New Territories (SENT) landfill in Hong Kong was capped and restored, by using 16 plant species growing on top of the final cover soil, during 1997-1999. In 2014, plant survey and soil properties analyses were conducted in a restored site (AT) and a natural site (CT, an undisturbed area, serving as a control). The similarity between the biota communities (i.e., plant and soil bacteria) of the two sites was assessed. Plant and soil bacterial communities at AT were significantly different (R=1, P<0.01, ANOSIM) from those at CT. A lower plant diversity but a higher soil bacterial diversity were observed at AT. The soil bacterial community structure was potentially driven by soil pH, moisture content, cation exchange capacity (CEC), N, and P. The engineered landfill had not been restored to an ecosystem similar to the natural environment 15years after restoration. Establishing similar soil properties in the landfill topsoil would be important to achieve a bacterial community similar to the natural area. This study can also offer a quick and inexpensive method for landfill engineers to assess the bacterial restoration of man-made ecosystems using plant and soil properties rather than DNA analyzing techniques.
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Affiliation(s)
- Xun-Wen Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
| | - James Tsz-Fung Wong
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
| | - Anna Oi-Wah Leung
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region, China.
| | - Charles Wang-Wai Ng
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
| | - Ming-Hung Wong
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China; Consortium on Health, Environment, Education and Research (CHEER), and Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong Special Administrative Region, China; School of Environment, Jinan University, Guangzhou, China.
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29
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Bouhajja E, Agathos SN, George IF. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnol Adv 2016; 34:1413-1426. [PMID: 27825829 DOI: 10.1016/j.biotechadv.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 12/23/2022]
Abstract
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.
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Affiliation(s)
- Emna Bouhajja
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium
| | - Spiros N Agathos
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech University, 100119 San Miguel de Urcuquí, Ecuador
| | - Isabelle F George
- Université Libre de Bruxelles, Laboratoire d'Ecologie des Systèmes Aquatiques, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
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30
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Jiang X, Takacs-Vesbach CD. Microbial community analysis of pH 4 thermal springs in Yellowstone National Park. Extremophiles 2016; 21:135-152. [PMID: 27807621 DOI: 10.1007/s00792-016-0889-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 10/20/2016] [Indexed: 02/01/2023]
Abstract
The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4-5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing. The taxonomic classification, based on 372 Mbp of unassembled metagenomic reads, indicated that this community included a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria, and Firmicutes. Functional comparison with other YNP thermal spring metagenomes indicated that the SMH metagenome was enriched in genes related to energy production and conversion, transcription, and carbohydrate transport. Analysis of genes involved in nitrogen metabolism revealed assimilatory and dissimilatory nitrate reduction pathways, whereas the majority of genes involved in sulfur metabolism were related to the reduction of sulfate to adenylylsulfate, sulfite, and H2S. Given that pH 4 thermal springs are relatively less common in YNP and thermal areas worldwide, they may harbor novel microbiota and the communities that inhabit them deserve further investigation.
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Affiliation(s)
- Xiaoben Jiang
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
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31
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Van Horn DJ, Wolf CR, Colman DR, Jiang X, Kohler TJ, McKnight DM, Stanish LF, Yazzie T, Takacs-Vesbach CD. Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw148. [PMID: 27495241 DOI: 10.1093/femsec/fiw148] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2016] [Indexed: 12/26/2022] Open
Abstract
Microbial consortia dominate glacial meltwater streams from polar regions, including the McMurdo Dry Valleys (MDV), where they thrive under physiologically stressful conditions. In this study, we examined microbial mat types and sediments found in 12 hydrologically diverse streams to describe the community diversity and composition within and across sites. Sequencing of the 16S rRNA gene from 129 samples revealed ∼24 000 operational taxonomic units (<97% DNA similarity), making streams the most biodiverse habitat in the MDV. Principal coordinate analyses revealed significant but weak clustering by mat type across all streams (ANOSIM R-statistic = 0.28) but stronger clustering within streams (ANOSIM R-statistic from 0.28 to 0.94). Significant relationships (P < 0.05) were found between bacterial diversity and mat ash-free dry mass, suggesting that diversity is related to the hydrologic regimes of the various streams, which are predictive of mat biomass. However, correlations between stream chemistry and community members were weak, possibly reflecting the importance of internal processes and hydrologic conditions. Collectively, these results suggest that localized conditions dictate bacterial community composition of the same mat types and sediments from different streams, and while MDV streams are hotspots of biodiversity in an otherwise depauperate landscape, controls on community structure are complex and site specific.
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Affiliation(s)
- David J Van Horn
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Caitlin R Wolf
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Daniel R Colman
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Xiaoben Jiang
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Prague 2, Prague, Czech Republic
| | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, 1560 30th Street, Boulder, CO 80303, USA
| | - Lee F Stanish
- National Ecological Observatory Network, 1685 38th Street, Boulder, CO, 80301
| | - Terrill Yazzie
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
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32
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Buelow HN, Winter AS, Van Horn DJ, Barrett JE, Gooseff MN, Schwartz E, Takacs-Vesbach CD. Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1040. [PMID: 27486436 PMCID: PMC4947590 DOI: 10.3389/fmicb.2016.01040] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.
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Affiliation(s)
- Heather N Buelow
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Ara S Winter
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - David J Van Horn
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - John E Barrett
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Michael N Gooseff
- Department of Civil, Architectural, and Environmental Engineering, Institute of Arctic and Alpine Research, University of Colorado Boulder Boulder, CO, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University Flagstaff, AZ, USA
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33
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Tytgat B, Verleyen E, Sweetlove M, D'hondt S, Clercx P, Van Ranst E, Peeters K, Roberts S, Namsaraev Z, Wilmotte A, Vyverman W, Willems A. Bacterial community composition in relation to bedrock type and macrobiota in soils from the Sør Rondane Mountains, East Antarctica. FEMS Microbiol Ecol 2016; 92:fiw126. [PMID: 27402710 DOI: 10.1093/femsec/fiw126] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 01/06/2023] Open
Abstract
Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high-altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analyzed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica), using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km(2) Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP-dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock.
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Affiliation(s)
- Bjorn Tytgat
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Sofie D'hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Pia Clercx
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Eric Van Ranst
- Laboratory of Soil Science, Department of Geology and Soil Science, Ghent University, 9000 Ghent, Belgium
| | - Karolien Peeters
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Stephen Roberts
- British Antarctic Survey, Natural Environment Research, Cambridge, CB3 0ET, UK
| | - Zorigto Namsaraev
- Department of Biotechnology and Bioenergy, NRC 'Kurchatov Institute', Moscow, 123182, Russia Winogradsky Institute of Microbiology RAS, Moscow, 117312, Russia
| | - Annick Wilmotte
- Centre for Protein Engineering, Department of Life Sciences, Liège University, 4000 Liège, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
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Nawaz A, Purahong W, Lehmann R, Herrmann M, Küsel K, Totsche KU, Buscot F, Wubet T. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities. Front Microbiol 2016; 7:666. [PMID: 27242696 PMCID: PMC4860458 DOI: 10.3389/fmicb.2016.00666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/21/2016] [Indexed: 11/13/2022] Open
Abstract
Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis.
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Affiliation(s)
- Ali Nawaz
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; Department of Biology, University of LeipzigLeipzig, Germany
| | - Witoon Purahong
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology Halle (Saale), Germany
| | - Robert Lehmann
- Institute of Geosciences, Friedrich Schiller University Jena Jena, Germany
| | - Martina Herrmann
- Institute of Ecology, Friedrich Schiller University Jena Jena, Germany
| | - Kirsten Küsel
- Institute of Ecology, Friedrich Schiller University JenaJena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Kai U Totsche
- Institute of Geosciences, Friedrich Schiller University Jena Jena, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil EcologyHalle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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Van Goethem MW, Makhalanyane TP, Valverde A, Cary SC, Cowan DA. Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw051. [DOI: 10.1093/femsec/fiw051] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
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Kohler TJ, Van Horn DJ, Darling JP, Takacs-Vesbach CD, McKnight DM. Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw049. [PMID: 26940086 DOI: 10.1093/femsec/fiw049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 01/06/2023] Open
Abstract
Microbial mats are abundant in many alpine and polar aquatic ecosystems. With warmer temperatures, new hydrologic pathways are developing in these regions and increasing dissolved nutrient fluxes. In the McMurdo Dry Valleys, thermokarsting may release both nutrients and sediment, and has the potential to influence mats in glacial meltwater streams. To test the role of nutrient inputs on community structure, we created nutrient diffusing substrata (NDS) with agar enriched in N, P and N + P, with controls, and deployed them into two Dry Valley streams. We found N amendments (N and N + P) to have greater chlorophyll-a concentrations, total algal biovolume, more fine filamentous cyanobacteria and a higher proportion of live diatoms than other treatments. Furthermore, N treatments were substantially elevated in Bacteroidetes and the small diatom, Fistulifera pelliculosa. On the other hand, species richness was almost double in P and N + P treatments over others, and coccoid green algae and Proteobacteria were more abundant in both streams. Collectively, these data suggest that nutrients have the potential to stimulate growth and alter community structure in glacial meltwater stream microbial mats, and the recent erosion of permafrost and accelerated glacial melt will likely impact resident biota in polar lotic systems here and elsewhere.
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Affiliation(s)
- Tyler J Kohler
- Institute of Arctic and Alpine Research, University of Colorado, 1560 30th Street, Boulder, CO 80303, USA Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Prague 2, Prague, Czech Republic
| | - David J Van Horn
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Joshua P Darling
- Institute of Arctic and Alpine Research, University of Colorado, 1560 30th Street, Boulder, CO 80303, USA
| | | | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, 1560 30th Street, Boulder, CO 80303, USA
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Okie JG, Van Horn DJ, Storch D, Barrett JE, Gooseff MN, Kopsova L, Takacs-Vesbach CD. Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities. Proc Biol Sci 2016; 282:20142630. [PMID: 26019154 DOI: 10.1098/rspb.2014.2630] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower temperatures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to contrasting α- and β-diversity patterns. In accord with the predictions, α-diversity, niche widths and occupancies decreased while β-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between α-diversity and pH and a negative relationship between α-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms.
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Affiliation(s)
- Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - David J Van Horn
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - David Storch
- Center for Theoretical Study, Charles University, Prague, Czech Republic Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic Department of Biological Sciences, Virginia Technological Institute, Blacksburg, VA, USA
| | - John E Barrett
- Department of Biological Sciences, Virginia Technological Institute, Blacksburg, VA, USA
| | - Michael N Gooseff
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - Lenka Kopsova
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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Chong CW, Pearce DA, Convey P. Emerging spatial patterns in Antarctic prokaryotes. Front Microbiol 2015; 6:1058. [PMID: 26483777 PMCID: PMC4588704 DOI: 10.3389/fmicb.2015.01058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.
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Affiliation(s)
- Chun-Wie Chong
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur Malaysia ; National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia
| | - David A Pearce
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne UK ; University Centre in Svalbard, Longyearbyen Norway ; British Antarctic Survey, Cambridge UK
| | - Peter Convey
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; British Antarctic Survey, Cambridge UK
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Hill R, Saetnan ER, Scullion J, Gwynn-Jones D, Ostle N, Edwards A. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure. Environ Microbiol 2015; 18:1942-53. [DOI: 10.1111/1462-2920.13017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Richard Hill
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
| | - Eli R. Saetnan
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - John Scullion
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Dylan Gwynn-Jones
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Nick Ostle
- Plant and Soil Ecology Laboratory; Lancaster Environmental Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
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40
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Gombeer S, Ramond JB, Eckardt FD, Seely M, Cowan DA. The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert. GEOBIOLOGY 2015; 13:494-505. [PMID: 25939371 DOI: 10.1111/gbi.12144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
Notwithstanding, the severe environmental conditions, deserts harbour a high diversity of adapted micro-organisms. In such oligotrophic environments, soil physicochemical characteristics play an important role in shaping indigenous microbial communities. This study investigates the edaphic bacterial communities of three contrasting desert terrain types (gravel plains, sand dunes and ephemeral rivers) with different surface geologies in the Central Namib Desert. For each site, we evaluated surface soil physicochemistries and used explorative T-RFLP methodology to get an indication of bacterial community diversities. While grain size was an important parameter in separating the three terrain types physicochemically and specific surface soil types could be distinguished, the desert edaphic bacterial communities displayed a high level of local spatial heterogeneity. Ten variables contributed significantly (P < 0.05) to the variance in the T-RFLP data sets: fine silt, medium and fine sand content, pH, S, Na, Zn, Al, V and Fe concentrations, and 40% of the total variance could be explained by these constraining variables. The results suggest that local physicochemical conditions play a significant role in shaping the bacterial structures in the Central Namib Desert and stress the importance of recording a wide variety of environmental descriptors to comprehensively assess the role of edaphic parameters in shaping microbial communities.
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Affiliation(s)
- S Gombeer
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - J-B Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - F D Eckardt
- Environmental and Geographical Science, Department of Geography, University of Cape Town, Cape Town, South Africa
| | - M Seely
- Gobabeb Research and Training Centre, Walvis Bay, Namibia
- School of Animal, Plant and Environmental Sciences (AP&ES), University of the Witwatersrand, Johannesburg, South Africa
| | - D A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute, University of Pretoria, Pretoria, South Africa
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Ji M, van Dorst J, Bissett A, Brown MV, Palmer AS, Snape I, Siciliano SD, Ferrari BC. Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. Polar Biol 2015. [DOI: 10.1007/s00300-015-1776-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Liu J, Wang J, Gao G, Bartlam MG, Wang Y. Distribution and diversity of fungi in freshwater sediments on a river catchment scale. Front Microbiol 2015; 6:329. [PMID: 25954259 PMCID: PMC4404825 DOI: 10.3389/fmicb.2015.00329] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Fungal communities perform essential functions in biogeochemical cycles. However, knowledge of fungal community structural changes in river ecosystems is still very limited. In the present study, we combined culture-dependent and culture-independent methods to investigate fungal distribution and diversity in sediment on a regional scale in the Songhua River catchment, located in North-East Asia. A total of 147 samples over the whole river catchment were analyzed. The results showed that compared to the mainstream, the tributaries have a higher fungal community organization and culturable fungal concentration, but possess lower community dynamics as assessed by denaturing gradient gel electrophoresis (DGGE). Furthermore, phylogenetic analysis of DGGE bands showed that Ascomycota and Basidiomycota were the predominant community in the Songhua River catchment. Redundancy analysis revealed that longitude was the primary factor determining the variation of fungal community structure, and fungal biomass was mainly related to the total nutrient content. Our findings provide new insights into the characteristics of fungal community distribution in a temperate zone river at a regional scale, and demonstrate that fungal dispersal is restricted by geographical barriers in a whole river catchment.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Jianan Wang
- Department of Environmental Science and Engineering, Nankai University Binhai College Tianjin, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
| | - Mark G Bartlam
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University Tianjin, China
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Kim M, Cho A, Lim HS, Hong SG, Kim JH, Lee J, Choi T, Ahn TS, Kim OS. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica. PLoS One 2015; 10:e0119966. [PMID: 25799273 PMCID: PMC4370865 DOI: 10.1371/journal.pone.0119966] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.
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Affiliation(s)
- Mincheol Kim
- Arctic Research Center, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Ahnna Cho
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Environmental Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyoun Soo Lim
- Department of Geological Sciences, Pusan National University, Busan, Republic of Korea
| | - Soon Gyu Hong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Ji Hee Kim
- Department of New Antarctic Station, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Joohan Lee
- Department of New Antarctic Station, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Taejin Choi
- Division of Climate Change, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Tae Seok Ahn
- Department of Environmental Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ok-Sun Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- * E-mail:
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Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. BMC Genomics 2015; 16:36. [PMID: 25649291 PMCID: PMC4326396 DOI: 10.1186/s12864-015-1220-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/02/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments. RESULTS Quantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. Notwithstanding genome incompleteness, these differences together with the decreased metabolic versatility are indicative of genome content scaling. CONCLUSIONS The genomes of the seven Antarctic Arthrobacter isolates contained several features that may be beneficial for growth and survival in the Antarctic soil environment, although these features were not unique to the Antarctic isolates. These genome sequences allow further investigations into the expression of physiological traits that enable survival under extreme conditions and, more importantly, into the ability of these bacteria to respond to future perturbations including climate change and human impacts.
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Affiliation(s)
- Melissa Dsouza
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Michael W Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Susan J Turner
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- BioDiscovery New Zealand Limited, Parnell, Auckland, New Zealand.
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Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus. PLoS One 2014; 9:e108009. [PMID: 25285990 PMCID: PMC4186907 DOI: 10.1371/journal.pone.0108009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/21/2014] [Indexed: 12/02/2022] Open
Abstract
Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR). However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs), primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further investigations into the expression of physiological attributes that enable survival under extreme conditions and selection processes that affect prokaryotic genome evolution.
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Affiliation(s)
- Melissa Dsouza
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan J. Turner
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- BioDiscovery New Zealand Limited, Parnell, Auckland, New Zealand
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46
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Narihiro T, Tamaki H, Akiba A, Takasaki K, Nakano K, Kamagata Y, Hanada S, Maji T. Microbial community structure of relict niter-beds previously used for saltpeter production. PLoS One 2014; 9:e104752. [PMID: 25111392 PMCID: PMC4128746 DOI: 10.1371/journal.pone.0104752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/14/2014] [Indexed: 11/24/2022] Open
Abstract
From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3−, Cl−, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB) and “Ca. Nitrososphaera”-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.
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Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Aya Akiba
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | | | | | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Taizo Maji
- Shubun University, Ichinomiya, Aichi, Japan
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47
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Tytgat B, Verleyen E, Obbels D, Peeters K, De Wever A, D’hondt S, De Meyer T, Van Criekinge W, Vyverman W, Willems A. Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats: a comparison between bidirectional pyrosequencing and cultivation. PLoS One 2014; 9:e97564. [PMID: 24887330 PMCID: PMC4041716 DOI: 10.1371/journal.pone.0097564] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/21/2014] [Indexed: 12/26/2022] Open
Abstract
The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1–22.2%) and OTU (3.5–3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1–V2 and V3–V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity.
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Affiliation(s)
- Bjorn Tytgat
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Dagmar Obbels
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Karolien Peeters
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Aaike De Wever
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie D’hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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48
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Schwartz E, Van Horn DJ, Buelow HN, Okie JG, Gooseff MN, Barrett JE, Takacs-Vesbach CD. Characterization of growing bacterial populations in McMurdo Dry Valley soils through stable isotope probing with (18) O-water. FEMS Microbiol Ecol 2014; 89:415-25. [PMID: 24785369 DOI: 10.1111/1574-6941.12349] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 02/21/2014] [Accepted: 04/24/2014] [Indexed: 02/01/2023] Open
Abstract
Soil microbial communities of the McMurdo Dry Valleys, Antarctica (MDV) contain representatives from at least fourteen bacterial phyla. However, given low rates of microbial activity, it is unclear whether this richness represents functioning rather than dormant members of the community. We used stable isotope probing (SIP) with (18) O-water to determine if microbial populations grow in MDV soils. Changes in the microbial community were characterized in soils amended with H2 (18) O and H2 (18) O-organic matter. Sequencing the 16S rRNA genes of the heavy and light fractions of the bacterial community DNA shows that DNA of microbial populations was labeled with (18) O-water, indicating these micro-organisms grew in the MDV soils. Significant differences existed in the community composition of the heavy and light fractions of the H2 (18) O and H2 (18) O-organic matter amended samples (Anosim P < 0.05 of weighted Unifrac distance). Control samples and the light DNA fraction of the H2 (18) O amended samples were dominated by representatives of the phyla Deinococcus-Thermus, Proteobacteria, Planctomyces, Gemmatimonadetes, Actinobacteria and Acidobacteria, whereas Proteobacteria were more prevalent in the heavy DNA fractions from the H2 (18) O-water and the H2 (18) O-water-organic matter treatments. Our results indicate that SIP with H2 (18) O can be used to distinguish active bacterial populations even in this low organic matter environment.
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Affiliation(s)
- Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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49
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Richter I, Herbold CW, Lee CK, McDonald IR, Barrett JE, Cary SC. Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2014; 89:347-59. [PMID: 24646164 DOI: 10.1111/1574-6941.12322] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/27/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022] Open
Abstract
Archaea are the least understood members of the microbial community in Antarctic mineral soils. Although their occurrence in Antarctic coastal soils has been previously documented, little is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (t-RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of soil physicochemical properties to characterize archaeal diversity and identify environmental factors that might shape and maintain archaeal communities in soils of the three southern most McMurdo Dry Valleys (Garwood, Marshall, and Miers Valley). Archaea were successfully detected in all inland and coastal mineral soils tested, revealing a low overall richness (mean of six operational taxonomic units [OTUs] per sample site). However, OTU richness was higher in some soils and this higher richness was positively correlated with soil water content, indicating water as a main driver of archaeal community richness. In total, 18 archaeal OTUs were detected, predominately Thaumarchaeota affiliated with Marine Group 1.1b (> 80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were loosely related to members of the phylum Euryarchaeota. This is the first comprehensive study showing a widespread presence and distribution of Archaea in inland Antarctic soils.
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Affiliation(s)
- Ingrid Richter
- School of Science, University of Waikato, Hamilton, New Zealand
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50
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van Dorst J, Bissett A, Palmer AS, Brown M, Snape I, Stark JS, Raymond B, McKinlay J, Ji M, Winsley T, Ferrari BC. Community fingerprinting in a sequencing world. FEMS Microbiol Ecol 2014; 89:316-30. [DOI: 10.1111/1574-6941.12308] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 01/25/2023] Open
Affiliation(s)
- Josie van Dorst
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | | | - Anne S. Palmer
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mark Brown
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Ian Snape
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Jonathan S. Stark
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Ben Raymond
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - John McKinlay
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
| | - Tristrom Winsley
- Australian Antarctic Division; Channel Highway; Kingston TAS Australia
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW Australia
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