51
|
Trofymow JA, Shay PE, Tomm B, Bérubé JA, Ramsfield T. Differences in Soil Fungal Communities between Forested Reclamation and Forestry Sites in the Alberta Oil Sands Region. J Fungi (Basel) 2023; 9:1110. [PMID: 37998915 PMCID: PMC10672713 DOI: 10.3390/jof9111110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Fungi play key roles in forest soils and provide benefits to trees via mycorrhizal symbioses. After severe disturbance, forest regrowth can be impeded because of changes in fungal communities. In 2013-2014, soil fungi in forest floor and mineral soil were examined by Roche 454 pyrosequencing in undisturbed, harvested, and burned jack pine stands in a forested area near Fort Chipewyan, Alberta. These fungal communities were compared with jack pine, white spruce, and larch stands in Gateway Hill, a nearby certified reclaimed area. In 2014, a more detailed sampling of forestry and reclamation jack pine sites examined fungi in soil fractions using two high-throughput sequencing platforms and a sporocarp survey. The significances of compositional and functional differences in fungal communities between the forested and reclamation sites were assessed using permutation tests of partially constrained ordinations, accounting for confounding factors by variance partitioning. Taxa associated with the forestry area were primarily ectomycorrhizal. Fungal richness and diversity were greater in soils from the reclamation sites and included significantly more pathogenic taxa and taxa with unknown functional properties. Fungal community dissimilarities may have been artefacts of historical legacies or, alternatively, may have resulted from contrasting niche differentiation between forestry and reclamation sites.
Collapse
Affiliation(s)
- John. A. Trofymow
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| | - Philip-Edouard Shay
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
- Canadian Wood Fibre Centre, Canadian Forest Service, 1350 Regent Street, Fredericton, NB E3B 5P7, Canada;
| | - Bradley Tomm
- Northern Forestry Centre, Canadian Forest Service, Natural Resources Canada, 5320-122nd Street, Edmonton, AB T6H 3S5, Canada; (B.T.); (T.R.)
| | - Jean A. Bérubé
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 Rue du Peps, Québec, QC G1V 4C7, Canada;
| | - Tod Ramsfield
- Northern Forestry Centre, Canadian Forest Service, Natural Resources Canada, 5320-122nd Street, Edmonton, AB T6H 3S5, Canada; (B.T.); (T.R.)
| |
Collapse
|
52
|
Papadopoulou E, Bekris F, Vasileiadis S, Krokida A, Rouvali T, Veskoukis AS, Liadaki K, Kouretas D, Karpouzas DG. Vineyard-mediated factors are still operative in spontaneous and commercial fermentations shaping the vinification microbial community and affecting the antioxidant and anticancer properties of wines. Food Res Int 2023; 173:113359. [PMID: 37803700 DOI: 10.1016/j.foodres.2023.113359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 10/08/2023]
Abstract
The grapevine and vinification microbiota have a strong influence on the characteristics of the produced wine. Currently we have a good understanding of the role of vineyard-associated factors, like cultivar, vintage and terroir in shaping the grapevine microbiota. Notwithstanding, their endurance along the vinification process remains unknown. Thus, the main objective of our study was to determine how these factors influence (a) microbial succession during fermentation (i.e., bacterial and fungal) and (b) the antioxidant, antimutagenic and anticancer potential of the produced wines. These were evaluated under different vinification strategies (i.e., spontaneous V1, spontaneous with preservatives V2, commercial V3), employed at near full-scale level by local wineries, for two cultivars (Roditis and Sideritis), two terroir types, and two vintages. Cultivar and vintage were strong and persistent determinants of the vinification microbiota, unlike terroir whose effect became weaker from the vineyard, and early fermentation stages, where non-Saccharomyces yeasts, filamentous fungi (i.e., Aureobasidium, Cladosporium, Lachancea, Alternaria, Aspergillus, Torulaspora) and acetic acid bacteria (AAB) (Gluconobacter, Acetobacter, Komagataeibacter) dominated, to late fermentation stages where Saccharomyces and Oenococcus become prevalent. Besides vineyard-mediated factors, the vinification process employed was the strongest determinant of the fungal community compared to the bacterial community were effects varied per cultivar. Vintage and vinification type were the strongest determinants of the antioxidant, antimutagenic and anticancer potential of the produced wines. Further analysis identified significant positive correlations between members of the vinification microbiota like the yeasts Torulaspora debrueckii and Lachancea quebecensis with the anticancer and the antioxidant properties of wines in both cultivars. These findings could be exploited towards a microbiota-modulated vinification process to produce high-quality wines with desirable properties and enhanced regional identity.
Collapse
Affiliation(s)
- Elena Papadopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | - Fotiοs Bekris
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | | | | | - Aristidis S Veskoukis
- University of Thessaly, Department of Nutrition and Dietetics, 42132 Trikala, Greece
| | - Kalliopi Liadaki
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece
| | - Demetrios Kouretas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Animal Physiology, 41500 Viopolis - Larissa, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, 41500 Viopolis - Larissa, Greece.
| |
Collapse
|
53
|
Li P, Tedersoo L, Crowther TW, Dumbrell AJ, Dini-Andreote F, Bahram M, Kuang L, Li T, Wu M, Jiang Y, Luan L, Saleem M, de Vries FT, Li Z, Wang B, Jiang J. Fossil-fuel-dependent scenarios could lead to a significant decline of global plant-beneficial bacteria abundance in soils by 2100. NATURE FOOD 2023; 4:996-1006. [PMID: 37904026 DOI: 10.1038/s43016-023-00869-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/29/2023] [Indexed: 11/01/2023]
Abstract
Exploiting the potential benefits of plant-associated microbes represents a sustainable approach to enhancing crop productivity. Plant-beneficial bacteria (PBB) provide multiple benefits to plants. However, the biogeography and community structure remain largely unknown. Here we constructed a PBB database to couple microbial taxonomy with their plant-beneficial traits and analysed the global atlas of potential PBB from 4,245 soil samples. We show that the diversity of PBB peaks in low-latitude regions, following a strong latitudinal diversity gradient. The distribution of potential PBB was primarily governed by environmental filtering, which was mainly determined by local climate. Our projections showed that fossil-fuel-dependent future scenarios would lead to a significant decline of potential PBB by 2100, especially biocontrol agents (-1.03%) and stress resistance bacteria (-0.61%), which may potentially threaten global food production and (agro)ecosystem services.
Collapse
Affiliation(s)
- Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | | | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Colchester, UK
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Mohammad Bahram
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Lu Kuang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Ting Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, USA
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, China.
| |
Collapse
|
54
|
Ren Z, Ye S, Li H, Huang X, Chen L, Cao S, Chen T. Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau. MICROBIAL ECOLOGY 2023; 86:2756-2769. [PMID: 37542537 DOI: 10.1007/s00248-023-02280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.
Collapse
Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 Beijing East Road, Nanjing, 210008, China.
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China.
| | - Shudan Ye
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Hongxuan Li
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Xilei Huang
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Luyao Chen
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Shengkui Cao
- School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Tao Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, 768 Jiayuguan W Road, Lanzhou, 730020, China.
| |
Collapse
|
55
|
Lu M, Luo X, Jiao JJ, Li H, Kuang X, Wang X, Feng Y, Zheng C. Uncovering the processes of microbial community assembly in the near-surface sediments of a climate-sensitive glacier-fed lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118714. [PMID: 37542806 DOI: 10.1016/j.jenvman.2023.118714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change. To fill this knowledge gap, this study systematically analyzed environmental variables, microbial communities, diversity, co-occurrence relationships, and community assembly processes in the near-surface sediments of a glacier-fed lake in the Tibetan Plateau. The results revealed distinct vertical gradients in microbial diversity and subcommunities, highlighting the significant influence of selection processes and adaptive abilities on microbial communities. Specifically, specialists played a crucial role within the overall microbial communities. Microbial assembly was primarily driven by homogeneous selection, but its influence declined with increasing depth. In contrast, homogenizing dispersal showed an opposite pattern, and the bottom layer exhibited heterogeneous selection and undominated processes. These patterns of microbial assembly were primarily driven by environmental gradients, with significant contributions from processes associated to ammonium and organic matter deposition, as well as chemical precipitation in response to a warming climate. This study enhances our understanding of the microbial communities and assembly processes in the near-surface sediments of glacier-fed lakes and sheds light on geo-microbiological processes in climate-sensitive lacustrine sediments.
Collapse
Affiliation(s)
- Meiqing Lu
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Luo
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China
| | - Jiu Jimmy Jiao
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China.
| | - Hailong Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xingxing Kuang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuejing Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuqing Feng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunmiao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| |
Collapse
|
56
|
Huang S, Lentendu G, Fujinuma J, Shiono T, Kubota Y, Mitchell EAD. Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication. MICROBIAL ECOLOGY 2023; 86:2606-2617. [PMID: 37458790 PMCID: PMC10640418 DOI: 10.1007/s00248-023-02259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/21/2023] [Indexed: 11/12/2023]
Abstract
The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.
Collapse
Affiliation(s)
- Shuyin Huang
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan.
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland.
| | - Junichi Fujinuma
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Takayuki Shiono
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan
| | - Yasuhiro Kubota
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
57
|
Wipulasena AYAP, Davison J, Helm A, Kasari L, Moora M, Prangel E, Reitalu T, Vahter T, Vasar M, Zobel M. Soil community composition in dynamic stages of semi-natural calcareous grassland. PLoS One 2023; 18:e0292425. [PMID: 37847721 PMCID: PMC10581465 DOI: 10.1371/journal.pone.0292425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
European dry thin-soil calcareous grasslands (alvars) are species-rich semi-natural habitats. Cessation of traditional management, such as mowing and grazing, leads to shrub and tree encroachment and the local extinction of characteristic alvar species. While soil microbes are known to play a critical role in driving vegetation and ecosystem dynamics, more information is needed about their composition and function in grasslands of different dynamic stages. Here we assess the composition of soil fungal, prokaryotic, and plant communities using soil environmental DNA from restored alvar grasslands in Estonia. The study areas included grasslands that had experienced different degrees of woody encroachment prior to restoration (woody plant removal and grazing), as well as unmanaged open grasslands. We found that, in general, different taxonomic groups exhibited correlated patterns of between-community variation. Previous forest sites, which had prior to restoration experienced a high degree of woody encroachment by ectomycorrhizal Scots pine, were compositionally most distinct from managed open grasslands, which had little woody vegetation even prior to restoration. The functional structure of plant and fungal communities varied in ways that were consistent with the representation of mycorrhizal types in the ecosystems prior to restoration. Compositional differences between managed and unmanaged open grasslands reflecting the implementation of grazing without further management interventions were clearer among fungal, and to an extent prokaryotic, communities than among plant communities. While previous studies have shown that during woody encroachment of alvar grassland, plant communities change first and fungal communities follow, our DNA-based results suggest that microbial communities reacted faster than plant communities during the restoration of grazing management in alvar grassland. We conclude that while the plant community responds faster to cessation of management, the fungal community responds faster to restoration of management. This may indicate hysteresis, where the eventual pathway back to the original state (grazed ecosystem) differs from the pathway taken towards the alternative state (abandoned semi-natural grassland ecosystem).
Collapse
Affiliation(s)
- A. Y. Ayesh Piyara Wipulasena
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Aveliina Helm
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Liis Kasari
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Elisabeth Prangel
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Triin Reitalu
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| |
Collapse
|
58
|
Li P, Tedersoo L, Crowther TW, Wang B, Shi Y, Kuang L, Li T, Wu M, Liu M, Luan L, Liu J, Li D, Li Y, Wang S, Saleem M, Dumbrell AJ, Li Z, Jiang J. Global diversity and biogeography of potential phytopathogenic fungi in a changing world. Nat Commun 2023; 14:6482. [PMID: 37838711 PMCID: PMC10576792 DOI: 10.1038/s41467-023-42142-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Phytopathogenic fungi threaten global food security but the ecological drivers of their global diversity and biogeography remain unknown. Here, we construct and analyse a global atlas of potential phytopathogenic fungi from 20,312 samples across all continents and major oceanic island regions, eleven land cover types, and twelve habitat types. We show a peak in the diversity of phytopathogenic fungi in mid-latitude regions, in contrast to the latitudinal diversity gradients observed in aboveground organisms. Our study identifies climate as an important driver of the global distribution of phytopathogenic fungi, and our models suggest that their diversity and invasion potential will increase globally by 2100. Importantly, phytopathogen diversity will increase largely in forest (37.27-79.12%) and cropland (34.93-82.51%) ecosystems, and this becomes more pronounced under fossil-fuelled industry dependent future scenarios. Thus, we recommend improved biomonitoring in forests and croplands, and optimised sustainable development approaches to reduce potential threats from phytopathogenic fungi.
Collapse
Affiliation(s)
- Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Thomas W Crowther
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China.
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lu Kuang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
| | - Ting Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Ming Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Dongzhen Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, 100091, Beijing, China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, 100091, Beijing, China
| | - Songhan Wang
- College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Colchester, Essex, UK.
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, 210095, Nanjing, China.
| |
Collapse
|
59
|
Ustick LJ, Larkin AA, Martiny AC. Global scale phylogeography of functional traits and microdiversity in Prochlorococcus. THE ISME JOURNAL 2023; 17:1671-1679. [PMID: 37454234 PMCID: PMC10504305 DOI: 10.1038/s41396-023-01469-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.
Collapse
Affiliation(s)
- Lucas J Ustick
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alyse A Larkin
- Department of Earth System Science, University of California Irvine, Irvine, CA, 92697, USA
- Global Ocean Monitoring and Observing, National Oceanic and Atmospheric Administration, Washington, DC, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
- Department of Earth System Science, University of California Irvine, Irvine, CA, 92697, USA.
| |
Collapse
|
60
|
Bier RL, Mosher JJ, Kaplan LA, Kan J. Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America. Environ Microbiol 2023; 25:1860-1874. [PMID: 37177981 DOI: 10.1111/1462-2920.16396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.
Collapse
Affiliation(s)
- Raven L Bier
- Stroud Water Research Center, Avondale, Pennsylvania, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
| | - Jennifer J Mosher
- Stroud Water Research Center, Avondale, Pennsylvania, USA
- Marshall University, Department of Biological Sciences, Huntington, West Virginia, USA
| | - Louis A Kaplan
- Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, Pennsylvania, USA
| |
Collapse
|
61
|
Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
Collapse
Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
62
|
Sagua MI, Nuozzi G, Sánchez ML, Huber P, Perdomo S, Schiaffino MR. Unraveling the effect of land use on the bacterioplankton community composition from highly impacted shallow lakes at a regional scale. FEMS Microbiol Ecol 2023; 99:fiad109. [PMID: 37715304 DOI: 10.1093/femsec/fiad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Bacterioplankton communities play a crucial role in global biogeochemical processes and are highly sensitive to changes induced by natural and anthropogenic stressors in aquatic ecosystems. We assessed the influence of Land Use Land Cover (LULC), environmental, and geographic changes on the bacterioplankton structure in highly connected and impacted shallow lakes within the Salado River basin, Buenos Aires, Argentina. Additionally, we investigated how changes in LULC affected the limnological characteristics of these lakes at a regional scale. Our analysis revealed that the lakes were ordinated by sub-basins (upper and lower) depending on their LULC characteristics and limnological properties. In coincidence, the same ordination was observed when considering the Bacterioplankton Community Composition (BCC). Spatial and environmental predictors significantly explained the variation in BCC, although when combined with LULC the effect was also important. While the pure LULC effect did not explain a significant percentage of BCC variation, the presence of atrazine in water, an anthropogenic variable linked to LULC, directly influenced both the BCC and some Amplicon Sequence Variants (ASVs) in particular. Our regional-scale approach contributes to understanding the complexity of factors driving bacterioplankton structure and how LULC pervasively affect these communities in highly impacted shallow lake ecosystems from the understudied Southern Hemisphere.
Collapse
Affiliation(s)
- Mara I Sagua
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - Guillermina Nuozzi
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - María L Sánchez
- CONICET - Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Intendente Guiraldes 2160 (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Intendente Guiraldes 2160 (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Huber
- Instituto Nacional de Limnología (INALI, CONICET-UNL). Colectora RN 168 Km 0 (3000), Paraje El Pozo, Santa Fe, Argentina
- Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luis S/N - Monjolinho (13565-905), São Carlos, São Paulo, Brazil
| | - Santiago Perdomo
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - María R Schiaffino
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| |
Collapse
|
63
|
Mioduchowska M, Pawłowska J, Mazanowski K, Weydmann-Zwolicka A. Contrasting Marine Microbial Communities of the Fram Strait with the First Confirmed Record of Cyanobacteria Prochlorococcus marinus in the Arctic Region. BIOLOGY 2023; 12:1246. [PMID: 37759645 PMCID: PMC10525857 DOI: 10.3390/biology12091246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The seawater microbiome is crucial in marine ecosystems because of its role in food chains and biogeochemical cycles; thus, we studied the composition of the pelagic marine microbiome collected in the upper 50 m on the opposite sides of Fram Strait: Spitsbergen and Greenland shelves. We found out that it differed significantly, with salinity being the main environmental variable responsible for these differences. The Spitsbergen shelf was dominated by Atlantic Waters, with a rather homogenous water column in terms of salinity and temperature down to 300 m; hence, the marine microbial community was also homogenous at all sampled depths (0, 25, 50 m). On the contrary, stations on the Greenland shelf were exposed to different water masses of both Arctic and Atlantic origin, which resulted in a more diverse microbial community there. Unexpectedly, for the very first time, we identified cyanobacterium Prochlorococcus marinus in Arctic waters (Spitsbergen shelf, 75-77° N). Till now, the distribution of this cyanobacteria in oceans has been described only between 40° N and 40° S. Considering the accelerated rate of climate warming in the Arctic, our results indicated that the seawater microbiome can be viewed as an amplifier of global change and that the Atlantification is in progress.
Collapse
Affiliation(s)
- Monika Mioduchowska
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdansk, 81-378 Gdynia, Poland;
| | - Joanna Pawłowska
- Department of Paleoceanography, Institute of Oceanology Polish Academy of Sciences, 81-712 Sopot, Poland;
| | - Karol Mazanowski
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdansk, 81-378 Gdynia, Poland;
| | - Agata Weydmann-Zwolicka
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdansk, 81-378 Gdynia, Poland;
| |
Collapse
|
64
|
Fine DH, Schreiner H. Oral microbial interactions from an ecological perspective: a narrative review. FRONTIERS IN ORAL HEALTH 2023; 4:1229118. [PMID: 37771470 PMCID: PMC10527376 DOI: 10.3389/froh.2023.1229118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Landscape ecology is a relatively new field of study within the sub-specialty of ecology that considers time and space in addition to structure and function. Landscape ecology contends that both the configuration (spatial pattern) and the composition (organisms both at the macro and or micro level) of an ecology can change over time. The oral cavity is an ideal place to study landscape ecology because of the variety of landscapes, the dynamic nature of plaque biofilm development, and the easy access to biofilm material. This review is intended to provide some specific clinical examples of how landscape ecology can influence the understanding of oral diseases and act as a supplement to diagnosis and treatment. The purpose of this review is two-fold; (1) to illustrate how landscape ecology can be used to clarify the two most prominent microbiologically induced infections in the oral cavity, and (2) how studies of oral microbiology can be used to enhance the understanding of landscape ecology. The review will distinguish between "habitat" and "niche" in a landscape and extend the concept that a "patch", is the demarcating unit of a habitat within a landscape. The review will describe how; (1) an individual patch, defined by its shape, edges and internal components can have an influence on species within the patch, (2) spatial dynamics over time within a patch can lead to variations or diversities of species within that patch space, and (3) an unwelcoming environment can promote species extinction or departure/dispersion into a more favorable habitat. Understanding this dynamic in relationship to caries and periodontal disease is the focus of this review.
Collapse
Affiliation(s)
- Daniel H. Fine
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States
| | | |
Collapse
|
65
|
Du H, Pan J, Zhang C, Yang X, Wang C, Lin X, Li J, Liu W, Zhou H, Yu X, Mo S, Zhang G, Zhao G, Qu W, Jiang C, Tian Y, He Z, Liu Y, Li M. Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America. Microbiol Spectr 2023; 11:e0157723. [PMID: 37668400 PMCID: PMC10580968 DOI: 10.1128/spectrum.01577-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/19/2023] [Indexed: 09/06/2023] Open
Abstract
As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.
Collapse
Affiliation(s)
- Huan Du
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xilan Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Cheng Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinhui Li
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Wan Liu
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Haokui Zhou
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoli Yu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Shuming Mo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Guoqing Zhang
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Guoping Zhao
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Chengjian Jiang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| |
Collapse
|
66
|
Johnson DB, Woolet J, Yedinak KM, Whitman T. Experimentally determined traits shape bacterial community composition one and five years following wildfire. Nat Ecol Evol 2023; 7:1419-1431. [PMID: 37524797 PMCID: PMC10482699 DOI: 10.1038/s41559-023-02135-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Wildfires represent major ecological disturbances, burning 2-3% of Earth's terrestrial area each year with sometimes drastic effects above- and belowground. Soil bacteria offer an ideal, yet understudied system within which to explore fundamental principles of fire ecology. To understand how wildfires restructure soil bacterial communities and alter their functioning, we sought to translate aboveground fire ecology to belowground systems by determining which microbial traits are important post-fire and whether changes in bacterial communities affect carbon cycling. We employed an uncommon approach to assigning bacterial traits, by first running three laboratory experiments to directly determine which microbes survive fires, grow quickly post-fire and/or thrive in the post-fire environment, while tracking CO2 emissions. We then quantified the abundance of taxa assigned to each trait in a large field dataset of soils one and five years after wildfires in the boreal forest of northern Canada. We found that fast-growing bacteria rapidly dominate post-fire soils but return to pre-burn relative abundances by five years post-fire. Although both fire survival and affinity for the post-fire environment were statistically significant predictors of post-fire community composition, neither are particularly influential. Our results from the incubation trials indicate that soil carbon fluxes post-wildfire are not likely limited by microbial communities, suggesting strong functional resilience. From these findings, we offer a traits-based framework of bacterial responses to wildfire.
Collapse
Affiliation(s)
| | - Jamie Woolet
- University of Wisconsin-Madison, Madison, WI, USA
- Colorado State University, Fort Collins, CO, USA
| | - Kara M Yedinak
- Forest Products Laboratory, USDA Forest Service, Madison, WI, USA
| | - Thea Whitman
- University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
67
|
Han D, Richter-Heitmann T, Kim JH, Friedrich MW, Yin X, Elvert M, Ryu JS, Jang K, Nam SI. Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments. Front Microbiol 2023; 14:1231839. [PMID: 37700860 PMCID: PMC10493304 DOI: 10.3389/fmicb.2023.1231839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.
Collapse
Affiliation(s)
- Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung-si, Gangwon-do, Republic of Korea
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ji-Hoon Kim
- Marine Geology & Energy Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, Republic of Korea
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Organic Geochemistry Group, Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jong-Sik Ryu
- Department of Earth and Environmental Sciences, Pukyong National University, Busan, Republic of Korea
| | - Kwangchul Jang
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Seung-Il Nam
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
| |
Collapse
|
68
|
Silverstein M, Bhatnagar JM, Segrè D. Metabolic complexity drives divergence in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551516. [PMID: 37577626 PMCID: PMC10418233 DOI: 10.1101/2023.08.03.551516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Microbial communities are shaped by the metabolites available in their environment, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. To this end, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the diverse assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively smaller ones, is necessary and sufficient to recapitulate all of our experimental observations. In addition to pointing to a fundamental principle of community assembly, the divergence-complexity effect has important implications for microbiome engineering applications, as it can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions.
Collapse
Affiliation(s)
- Michael Silverstein
- Bioinformatics Program, Boston University, Boston, MA
- Biological Design Center, Boston University, Boston, MA
| | - Jennifer M. Bhatnagar
- Bioinformatics Program, Boston University, Boston, MA
- Department of Biology, Boston University, Boston, MA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA
- Biological Design Center, Boston University, Boston, MA
- Department of Biology, Boston University, Boston, MA
- Department of Biomedical Engineering and Department of Physics, Boston University, Boston, MA
| |
Collapse
|
69
|
Ren Y, Shao Q, Ge W, Li X, Wang H, Dong C, Zhang Y, Deshmukh SK, Han Y. Assembly Processes and Biogeographical Characteristics of Soil Bacterial Sub-communities of Different Habitats in Urban Green Spaces. Curr Microbiol 2023; 80:309. [PMID: 37535152 DOI: 10.1007/s00284-023-03428-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/23/2023] [Indexed: 08/04/2023]
Abstract
The process of urbanization is one of the most important human-driven activities that reshape the natural distribution of soil microorganisms. However, it is still unclear about the effects of urbanization on the different taxonomic soil bacterial community dynamics. In this study, we collected soil samples from highly urbanized the regions of Yangtze River Delta, Beijing-Tianjin-Hebei in China, to explore the bio-geographic patterns, assembly processes, and symbiotic patterns of abundant, moderate, and rare bacterial communities. We found that the number of moderate and rare taxa species were lower than that of abundant taxa, but their α-diversity index was higher than abundant taxa. Proteobacteria, Acidobacteria, Actinobacteria, Bacterioidetes, and Chloroflexi were the dominant phylum across all three sub-communities. And the β-diversity value of rare taxa was significantly higher than those of moderate and abundant taxa. Abundant, moderate, and rare sub-communities showed a weak distance-decay relationship, and the moderate taxa had the highest turnover rate of microbial geography in the context of urbanization. Diffusion limitation was the dominant process of soil bacterial community assembly. The co-occurrence networks of abundant, moderate, and rare taxa were dominated by positive correlations. The network of moderate taxa had the highest modularity, followed by abundant taxa. The main functions of the abundant, moderate, and rare taxa were related to Chemoheterotrophy and N transformations. Redundancy analysis showed that the dispersal limitation, climate, and soil properties were the main factors dominating bio-geographic differences in soil bacterial community diversity. We conclude that human-dominated urbanization processes have generated more uncertain survival pressures on soil bacteria, which resulted in a stronger linkage but weak bio-geographic variation for soil bacteria. In the future urban planning process, we suggest that such maintenance of native vegetation and soil types should be considered to maintain the long-term stability of local microbial ecosystem functions.
Collapse
Affiliation(s)
- Yulian Ren
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Wei Ge
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xin Li
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Haiyan Wang
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yanwei Zhang
- School of Biological Sciences, Guizhou Education University, Guiyang, 550018, Guizhou, China
| | - Sunil Kumar Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China.
| |
Collapse
|
70
|
Yang K, Qin PH, Yuan MY, Chen L, Zhang YJ, Chu D. Infection density pattern of Cardinium affects the responses of bacterial communities in an invasive whitefly under heat conditions. INSECT SCIENCE 2023; 30:1149-1164. [PMID: 36331043 DOI: 10.1111/1744-7917.13141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Communities of bacteria, especially symbionts, are vital for the growth and development of insects and other arthropods, including Bemisia tabaci Mediterranean (MED), a destructive and invasive insect pest. However, the infection density patterns and influence factors of bacteria in whiteflies, which mainly include symbionts, remain largely unclear. To reveal the different density patterns of Cardinium in B. tabaci MED populations and the impacts of high temperatures on whiteflies with different Cardinium density infection patterns, 2 isofemale lines isolated from B. tabaci MED from the same geographical population of China and from B. tabaci MED collected from other countries and locations were examined using several techniques and methods, including fluorescence in situ hybridization (FISH), quantitative real-time polymerase chain reaction (qPCR), 16S rRNA gene sequencing, and 2b-RAD sequencing. The results showed that there were 2 different infection density patterns of Cardinium in B. tabaci MED (including 1 high-density pattern and 1 low-density pattern). For whiteflies with low-density Cardinium, conventional PCR could not detect Cardinium, but the other techniques confirmed that there was a low level of Cardinium within hosts. High temperature significantly decreased the diversity of bacterial communities: the relative titer of Cardinium increased but the density of Rickettsia decreased in the isofemale line with high-density Cardinium. However, high temperature did not influence the diversity and symbiont density in the line with low-density Cardinium. Moreover, high temperature influenced the functions of bacterial communities in whiteflies with high-density Cardinium but did not affect the bacterial functions in whiteflies with low-density Cardinium. Our results provide novel insights into the complex associations between symbionts and host insects.
Collapse
Affiliation(s)
- Kun Yang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Peng-Hao Qin
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Meng-Ying Yuan
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - You-Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| |
Collapse
|
71
|
He Y, Pan J, Huang D, Sanford RA, Peng S, Wei N, Sun W, Shi L, Jiang Z, Jiang Y, Hu Y, Li S, Li Y, Li M, Dong Y. Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering. ENVIRONMENT INTERNATIONAL 2023; 178:108067. [PMID: 37393724 DOI: 10.1016/j.envint.2023.108067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca2+ concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H+ antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.
Collapse
Affiliation(s)
- Yu He
- School of Environmental Studies, China University of Geosciences, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Studies, Shenzhen University, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, China
| | - Dongmei Huang
- School of Environmental Studies, China University of Geosciences, China; Yejin Geological Team of Hubei Geological Bureau, China
| | - Robert A Sanford
- Department of Earth Science & Environmental Change, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Shuming Peng
- Institute of Ecological Environment, Chengdu University of Technology, China
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Weimin Sun
- Guangdong Institute of Eco-environmental and Soil Science, Guangdong, China
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, China
| | - Yongguang Jiang
- School of Environmental Studies, China University of Geosciences, China
| | - Yidan Hu
- School of Environmental Studies, China University of Geosciences, China
| | - Shuyi Li
- School of Environmental Studies, China University of Geosciences, China
| | - Yongzhe Li
- School of Environmental Studies, China University of Geosciences, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Studies, Shenzhen University, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, China.
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China; Hubei Key Laboratory of Wetland Evolution and Ecology Restoration, China.
| |
Collapse
|
72
|
Li H, Zhou H, Yang S, Dai X. Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities. Appl Environ Microbiol 2023; 89:e0070123. [PMID: 37404136 PMCID: PMC10370332 DOI: 10.1128/aem.00701-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.
Collapse
Affiliation(s)
- Haizhou Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shanshan Yang
- College of Marine Science and Technology, China University of Geosciences, Wuhan, Hubei, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institutes of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
73
|
Lodhi AF, Zhang Y, Adil M, Deng Y. Design and application of a novel culturing chip (cChip) for culturing the uncultured aquatic microorganisms. Arch Microbiol 2023; 205:285. [PMID: 37442830 DOI: 10.1007/s00203-023-03613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Culturing uncultured microorganisms is an important aspect of microbiology. Once cultured, these microorganisms can be a source of useful antibiotics, enzymes etc. In this study, we have designed a novel culturing chip (cChip) to facilitate the growth of uncultured aquatic bacterial community by concentrating the samples. cChip was optimized for microbial growth using known bacteria in the laboratory as a pre-experiment. Then microorganisms from a freshwater lake were concentrated and inoculated, before putting the inoculated cChip in a simulated lake environment and further sub-culturing on laboratory media. High-throughput sequencing and traditional culturing were also performed for comparison. These three methods were able to detect 265 genera of microorganisms in the sample, of which 78.87% were detected by high-throughput sequencing, 30.94% by cChip, while only 6.42% were obtained by traditional culture. Moreover, all microorganisms obtained by traditional culture were also cultured using the cChip. A total of 45 new strains were isolated from the cChip, and their 16S rRNA gene sequences were 91.35% to 98.7% similar to their closest relatives according to NCBI GenBank database. We conclude that the design and simple operation of cChip can improve the culture efficiency of traditional culture by almost 5 times. To the best of our knowledge, this is the first report comparing a novel culturing method with high-throughput sequencing data and traditional culturing of the same samples.
Collapse
Affiliation(s)
- Adil Farooq Lodhi
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Ying Zhang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Maria Adil
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| |
Collapse
|
74
|
Gonzalez JM, Aranda B. Microbial Growth under Limiting Conditions-Future Perspectives. Microorganisms 2023; 11:1641. [PMID: 37512814 PMCID: PMC10383181 DOI: 10.3390/microorganisms11071641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.
Collapse
Affiliation(s)
- Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
| | - Beatriz Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
| |
Collapse
|
75
|
Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
Collapse
Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
| | | | | |
Collapse
|
76
|
Sun X, Sharon O, Sharon A. Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses. Microbiol Spectr 2023; 11:e0061123. [PMID: 37166321 PMCID: PMC10269846 DOI: 10.1128/spectrum.00611-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.
Collapse
Affiliation(s)
- Xiang Sun
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Or Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
77
|
Ren L, Song X, Wu C, Li G, Zhang X, Xia X, Xiang C, Han BP, Jeppesen E, Wu QL. Biogeographical and Biodiversity Patterns of Marine Planktonic Bacteria Spanning from the South China Sea across the Gulf of Bengal to the Northern Arabian Sea. Microbiol Spectr 2023; 11:e0039823. [PMID: 37098981 PMCID: PMC10269852 DOI: 10.1128/spectrum.00398-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023] Open
Abstract
Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll a are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll a gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll a concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of Prochlorococcus, the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll a concentrations (>0.5 μg/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll a relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll a than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll a concentrations. Higher chlorophyll a concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication. IMPORTANCE One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll a relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.
Collapse
Affiliation(s)
- Lijuan Ren
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xingyu Song
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chuangfeng Wu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiufeng Zhang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chenhui Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Key Laboratory of Science and Technology on Operational Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Erik Jeppesen
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
- Department of Bioscience, Aarhus University, Silkeborg, Denmark
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Turkey
| | - Qinglong L. Wu
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
78
|
Kim HS, Park K, Jo HY, Kwon MJ. Weathering extents and anthropogenic influences shape the soil bacterial community along a subsurface zonation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162570. [PMID: 36889395 DOI: 10.1016/j.scitotenv.2023.162570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Subsurface environments are composed of various active soil layers with dynamic biogeochemical interactions. We investigated soil bacterial community composition and geochemical properties along a vertical soil profile, which was categorized into surface, unsaturated, groundwater fluctuated, and saturated zones, in a testbed site formerly used as farmland for several decades. We hypothesized that weathering extent and anthropogenic inputs influence changes in the community structure and assembly processes and have distinct contributions along the subsurface zonation. Elemental distribution in each zone was strongly affected by the extent of chemical weathering. A 16S rRNA gene analysis indicated that bacterial richness (alpha diversity) was highest in the surface zone, and also higher in the fluctuated zone, than in unsaturated and saturated zones due to the effects of high organic matter, high nutrient levels, and/or aerobic conditions. Redundancy analysis showed that major elements (P, Na), a trace element (Pb), NO3, and the weathering extent were key driving forces shaping bacterial community composition along the subsurface zonation. Assembly processes were governed by specific ecological niches, such as homogeneous selection, in the unsaturated, fluctuated, and saturated zones, while in the surface zone, they were dominated by dispersal limitation. These findings together suggest that the vertical variation in soil bacterial community assembly is zone-specific and shaped by the relative influences of deterministic vs. stochastic processes. Our results provide novel insights into the relationships between bacterial communities, environmental factors, and anthropogenic influences (e.g., fertilization, groundwater, soil contamination), and into the roles of specific ecological niches and subsurface biogeochemical processes in these relationships.
Collapse
Affiliation(s)
- Han-Suk Kim
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kanghyun Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
| |
Collapse
|
79
|
Vagelas I, Reizopoulou A, Exadactylos A, Madesis P, Karapetsi L, Michail G. Stalactites Core Prospect as Environmental "Microbial Ark": The Actinomycetota Diversity Paradigm, First Reported from a Greek Cave. Pol J Microbiol 2023; 72:155-168. [PMID: 37314357 DOI: 10.33073/pjm-2023-016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/15/2023] [Indexed: 06/15/2023] Open
Abstract
Speleothems found in caves worldwide are considered the natural libraries of paleontology. Bacteria found in these ecosystems are generally limited to Proteobacteria and Actinomycetota, but rare microbiome and "Dark Matter" is generally under-investigated and often neglected. This research article discusses, for the first time to our knowledge, the diachronic diversity of Actinomycetota entrapped inside a cave stalactite. The planet's environmental microbial community profile of different eras can be stored in these refugia (speleothems). These speleothems could be an environmental "Microbial Ark" storing rare microbiome and "Dark Matter" bacterial communities evermore.
Collapse
Affiliation(s)
- Ioannis Vagelas
- 2Laboratory of Plant Pathology, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Angeliki Reizopoulou
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Panagiotis Madesis
- 3Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Lefkothea Karapetsi
- 3Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
- 4Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), Thessaloniki, Greece
| | - George Michail
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| |
Collapse
|
80
|
Hauer MA, Breusing C, Trembath-Reichert E, Huber JA, Beinart RA. Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts. MICROBIOME 2023; 11:106. [PMID: 37189129 DOI: 10.1186/s40168-023-01493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/11/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Marine symbioses are predominantly established through horizontal acquisition of microbial symbionts from the environment. However, genetic and functional comparisons of free-living populations of symbionts to their host-associated counterparts are sparse. Here, we assembled the first genomes of the chemoautotrophic gammaproteobacterial symbionts affiliated with the deep-sea snail Alviniconcha hessleri from two separate hydrothermal vent fields of the Mariana Back-Arc Basin. We used phylogenomic and population genomic methods to assess sequence and gene content variation between free-living and host-associated symbionts. RESULTS Our phylogenomic analyses show that the free-living and host-associated symbionts of A. hessleri from both vent fields are populations of monophyletic strains from a single species. Furthermore, genetic structure and gene content analyses indicate that these symbiont populations are differentiated by vent field rather than by lifestyle. CONCLUSION Together, this work suggests that, despite the potential influence of host-mediated acquisition and release processes on horizontally transmitted symbionts, geographic isolation and/or adaptation to local habitat conditions are important determinants of symbiont population structure and intra-host composition. Video Abstract.
Collapse
Affiliation(s)
- Michelle A Hauer
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | | | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Falmouth, MA, USA
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA.
| |
Collapse
|
81
|
Russell MJ. A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism. Front Microbiol 2023; 14:1145915. [PMID: 37275164 PMCID: PMC10236563 DOI: 10.3389/fmicb.2023.1145915] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/22/2023] [Indexed: 06/07/2023] Open
Abstract
The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.
Collapse
Affiliation(s)
- Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, Torino, Italy
| |
Collapse
|
82
|
Sprockett DD, Price JD, Juritsch AF, Schmaltz RJ, Real MV, Goldman SL, Sheehan M, Ramer-Tait AE, Moeller AH. Home-site advantage for host species-specific gut microbiota. SCIENCE ADVANCES 2023; 9:eadf5499. [PMID: 37184968 PMCID: PMC10184861 DOI: 10.1126/sciadv.adf5499] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1-/- mice, indicating home-site advantage for native microbiota independent of host adaptive immunity. However, a minority of native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1-/- hosts, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates home-site advantage for native gut bacteria, consistent with local adaptation of gut microbiota to their mammalian species.
Collapse
Affiliation(s)
- Daniel D. Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeffrey D. Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anthony F. Juritsch
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Robert J. Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madalena V. F. Real
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Michael Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
83
|
Pulido-Suárez L, Notario Del Pino J, Díaz-Peña FJ, Perdomo-González A, González-Rodríguez ÁM, León-Barrios M. High Diversity of Bradyrhizobial Species Fix Nitrogen with Woody Legume Spartocytisus supranubius in a High Mountain Ecosystem. Microorganisms 2023; 11:1244. [PMID: 37317218 DOI: 10.3390/microorganisms11051244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
The symbiosis between rhizobia and legumes is of pivotal importance in nitrogen-poor ecosystems. Furthermore, as it is a specific process (most legumes only establish a symbiosis with certain rhizobia), it is of great interest to know which rhizobia are able to nodulate key legumes in a specific habitat. This study describes the diversity of the rhizobia that are able to nodulate the shrub legume Spartocytisus supranubius in the harsh environmental conditions of the high mountain ecosystem of Teide National Park (Tenerife). The diversity of microsymbionts nodulating S. supranubius was estimated from a phylogenetic analysis of root nodule bacteria isolated from soils at three selected locations in the park. The results showed that a high diversity of species of Bradyrhizobium and two symbiovars can nodulate this legume. Phylogenies of ribosomal and housekeeping genes showed these strains distributed into three main clusters and a few isolates on separate branches. These clusters consist of strains representing three new phylogenetic lineages of the genus Bradyrhizobium. Two of these lineages belong to the B. japonicum superclade, which we refer to as B. canariense-like and B. hipponense-like, as the type strains of these species are the closest species to our isolates. The third main group was clustered within the B. elkanii superclade and is referred to as B. algeriense-like as B. algeriense is its closest species. This is the first time that bradyrhizobia of the B. elkanii superclade have been reported for the canarian genista. Furthermore, our results suggest that these three main groups might belong to potential new species of the genus Bradyrhizobium. Analysis of the soil physicochemical properties of the three study sites showed some significant differences in several parameters, which, however, did not have a major influence on the distribution of bradyrhizobial genotypes at the different locations. The B. algeriense-like group had a more restrictive distribution pattern, while the other two lineages were detected in all of the soils. This suggests that the microsymbionts are well adapted to the harsh environmental conditions of Teide National Park.
Collapse
Affiliation(s)
- Laura Pulido-Suárez
- Department of Biochemistry, Microbiology, Genetics and Cellular Biology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Jesús Notario Del Pino
- Department of Animal Biology, Soil Science and Geology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Francisco J Díaz-Peña
- Department of Animal Biology, Soil Science and Geology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Adolfo Perdomo-González
- Department of Animal Biology, Soil Science and Geology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Águeda M González-Rodríguez
- Department of Botany, Ecology and Plant Physiology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - Milagros León-Barrios
- Department of Biochemistry, Microbiology, Genetics and Cellular Biology, University of La Laguna, 38200 San Cristóbal de La Laguna, Spain
| |
Collapse
|
84
|
Dai W, Liu Y, Yao D, Wang N, Ye X, Cui Z, Wang H. Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161680. [PMID: 36682558 DOI: 10.1016/j.scitotenv.2023.161680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/03/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.
Collapse
Affiliation(s)
- Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China.
| |
Collapse
|
85
|
Riley AB, Grillo MA, Epstein B, Tiffin P, Heath KD. Discordant population structure among rhizobium divided genomes and their legume hosts. Mol Ecol 2023; 32:2646-2659. [PMID: 36161739 DOI: 10.1111/mec.16704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.
Collapse
Affiliation(s)
- Alex B Riley
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| |
Collapse
|
86
|
Deng W, Zhang F, Li YP, Zhang X, Fornacca D, Yang XY, Xiao W. Uncovering the biogeographic pattern of the widespread nematode-trapping fungi Arthrobotrys oligospora: watershed is the key. Front Microbiol 2023; 14:1152751. [PMID: 37152762 PMCID: PMC10156993 DOI: 10.3389/fmicb.2023.1152751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Studies of biogeographic patterns of fungi have long been behind those of plants and animals. The presence of worldwide species, the lack of systematic sampling design and adequate sampling effort, and the lack of research units are responsible for this status. This study investigates the biogeographical patterns of Arthrobotrys oligospora, the most widespread globally distributed nematode-trapping fungi (NTF), by stratified collecting and analyzing 2,250 samples from 228 sites in Yunnan Province, China. The A. oligospora was isolated, and 149 strains were subjected to ITS, TUB, TEF and RPB2 gene sequencing and multi-gene association phylogeographic analysis. The results show that at population level A. oligospora is randomly distributed throughout Yunnan Province and has no biogeographical distribution pattern. At the genetic level, the phylogenetic tree of A. oligospora diverges into five major evolutionary clades, with a low degree of gene flow between the five clades. However, the correlation between the phylogenetic diversity of A. oligospora and geographical factors was low. There was no clear pattern in the phylogenetic clades distribution of A. oligospora either without dividing the study unit or when the grid was used as the study unit. When watersheds were used as the study unit, 67.4%, 63.3%, 65.9%, 83.3%, and 66.7% of clade 1-5 strains were distributed in the Jinsha river, Red river, Peal river, Lancang river, and Nujiang-Irawaddy river watersheds, respectively. The clades distribution of A. oligospora was highly consistent with the watersheds distribution. Training predictions of the clades distributions using randomly generated polygons were also less accurate than watersheds. These results suggest that watersheds are key to discovering the biogeographic distribution patterns of A. oligospora. The A. oligospora populations are blocked by mountains in the watershed, and gene flow barriers have occurred, which may have resulted in the formation of multiple cryptic species. Watersheds are also ideal for understanding such speciation processes, explaining factors affecting biodiversity distribution and coupling studies of plant and animal and microbial diversity.
Collapse
Affiliation(s)
- Wei Deng
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Yan-Peng Li
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali, Yunnan, China
| | - Xin Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Davide Fornacca
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, Yunnan, China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali, Yunnan, China
| |
Collapse
|
87
|
Zhang Z, Li J, Li H, Wang L, Zhou Y, Li S, Zhang Z, Feng K, Deng Y. Environmental DNA metabarcoding reveals the influence of human activities on microeukaryotic plankton along the Chinese coastline. WATER RESEARCH 2023; 233:119730. [PMID: 36801577 DOI: 10.1016/j.watres.2023.119730] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Microeukaryotic plankton, with its extremely diverse taxa, is a key component in both the marine food web and biogeochemical cycling. Coastal seas, which are home to the numerous microeukaryotic plankton that underpin the functions of these aquatic ecosystems, are often impacted by human activities. However, understanding the biogeographical patterns of diversity and community structure of microeukaryotic plankton and the role that major shaping factors play at the continent scale is still a challenge in coastal ecology. Here, the biogeographic patterns of biodiversity, community structure, and co-occurrence patterns were investigated by environmental DNA (eDNA) based approaches. Unlike most eDNA studies, we combined several methods (in silico PCR, mock and environmental communities) to systematically evaluate the specificity and coverage of primers to overcome the limitation of marker selection on biodiversity recovery. The 1380F/1510R primer set showed the best performance for the amplification of coastal plankton with the highest coverage, sensitivity, and resolution. We showed a unimodal pattern for planktonic alpha diversity with latitude (P < 0.001), and nutrient-related factors (NO3N, NO2N, and NH4N) were the leading predictors for spatial patterning. Significant regional biogeographic patterns and potential drivers for planktonic communities were found across coastal regions. All communities generally fitted the regional distance-decay relationship (DDR) model with the strongest spatial turnover rate was found in the Yalujiang (YLJ) estuary (P < 0.001). The environmental factors, especially inorganic nitrogen and heavy metals (HMs), had the greatest impact on planktonic community similarity in the Beibu Bay (BB) and East China Sea (ECS). Furthermore, we observed spatial plankton co-occurrence patterns, and the networked topology and structure were strongly driven by potential anthropogenic activity factors (nutrients and HMs). Overall, our study provided a systematic approach for metabarcode primer selection in eDNA-based biodiversity monitoring and revealed that the spatial pattern of the microeukaryotic plankton community was mainly controlled by regional human activity-related factors.
Collapse
Affiliation(s)
- Zheng Zhang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jiang Li
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources; Key Laboratory of Ecological Environment Science and Technology, Ministry of Natural Resources, Qingdao, China, 266061.
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Linlin Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science College of Environmental and Natural Resource Sciences, Zhejiang University, China
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.
| |
Collapse
|
88
|
Du X, Gu S, Zhang Z, Li S, Zhou Y, Zhang Z, Zhang Q, Wang L, Ju Z, Yan C, Li T, Wang D, Yang X, Peng X, Deng Y. Spatial distribution patterns across multiple microbial taxonomic groups. ENVIRONMENTAL RESEARCH 2023; 223:115470. [PMID: 36775088 DOI: 10.1016/j.envres.2023.115470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R2 = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.
Collapse
Affiliation(s)
- Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Zheng Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yuqi Zhou
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhaojing Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Qi Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Linlin Wang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhicheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengliang Yan
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
89
|
Chase AB, Bogdanov A, Demko AM, Jensen PR. Biogeographic patterns of biosynthetic potential and specialized metabolites in marine sediments. THE ISME JOURNAL 2023:10.1038/s41396-023-01410-3. [PMID: 37061583 DOI: 10.1038/s41396-023-01410-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023]
Abstract
While the field of microbial biogeography has largely focused on the contributions of abiotic factors to community patterns, the potential influence of biotic interactions in structuring microbial communities, such as those mediated by the production of specialized metabolites, remains largely unknown. Here, we examined the relationship between microbial community structure and specialized metabolism at local spatial scales in marine sediment samples collected from the Long-Term Ecological Research (LTER) site in Moorea, French Polynesia. By employing a multi-omic approach to characterize the taxonomic, functional, and specialized metabolite composition within sediment communities, we find that biogeographic patterns were driven by local scale processes (e.g., biotic interactions) and largely independent of dispersal limitation. Specifically, we observed high variation in biosynthetic potential (based on Bray-Curtis dissimilarity) between samples, even within 1 m2 plots, that reflected uncharacterized chemical space associated with site-specific metabolomes. Ultimately, connecting biosynthetic potential to community metabolomes facilitated the in situ detection of natural products and revealed new insights into the complex metabolic dynamics associated with sediment microbial communities. Our study demonstrates the potential to integrate biosynthetic genes and metabolite production into assessments of microbial community dynamics.
Collapse
Affiliation(s)
- Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, USA.
| | - Alexander Bogdanov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
| |
Collapse
|
90
|
Liang Q, Mod HK, Luo S, Ma B, Yang K, Chen B, Qi W, Zhao Z, Du G, Guisan A, Ma X, Le Roux X. Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition. Mol Ecol 2023. [PMID: 37060060 DOI: 10.1111/mec.16952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023]
Abstract
The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.
Collapse
Affiliation(s)
- Qingqing Liang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Shuaiwei Luo
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Beibei Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kena Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Beibei Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wei Qi
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhigang Zhao
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xavier Le Roux
- INRAE, Université de Lyon, Université Lyon 1, CNRS, vetAgroSup, UMR 1418 INRAE, UMR 5557 CNRS, Ecologie Microbienne LEM, Villeurbanne, France
| |
Collapse
|
91
|
Deng W, Zhang F, Fornacca D, Yang XY, Xiao W. Those Nematode-Trapping Fungi That are not Everywhere: Hints Towards Soil Microbial Biogeography. J Microbiol 2023:10.1007/s12275-023-00043-7. [PMID: 37022590 DOI: 10.1007/s12275-023-00043-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/07/2023]
Abstract
The existence of biogeography for microorganisms is a raising topic in ecology and researchers are employing better distinctions between single species, including the most rare ones, to reveal potential hidden patterns. An important volume of evidence supporting heterogeneous distributions for bacteria, archaea and protists is accumulating, and more recently a few efforts have targeted microscopic fungi. We propose an insight into this latter kingdom by looking at a group of soil nematode-trapping fungi whose species are well-known and easily recognizable. We chose a pure culture approach because of its reliable isolation procedures for this specific group. After morphologically and molecularly identifying all species collected from 2250 samples distributed in 228 locations across Yunnan province of China, we analyzed occurrence frequencies and mapped species, genera, and richness. Results showed an apparent cosmopolitan tendency for this group of fungi, including species richness among sites. However, only four species were widespread across the region, while non-random heterogeneous distributions were observed for the remaining 40 species, both in terms of statistical distribution of species richness reflected by a significant variance-to-mean ratio, as well as in terms of visually discernible spatial clusters of rare species and genera on the map. Moreover, several species were restricted to only one location, raising the question of whether endemicity exists for this microbial group. Finally, environmental heterogeneity showed a marginal contribution in explaining restricted distributions, suggesting that other factors such as geographical isolation and dispersal capabilities should be explored. These findings contribute to our understanding of the cryptic geographic distribution of microorganisms and encourage further research in this direction.
Collapse
Affiliation(s)
- Wei Deng
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, People's Republic of China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, People's Republic of China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, 671003, Yunnan, People's Republic of China
| | - Fa Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, People's Republic of China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, People's Republic of China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, 671003, Yunnan, People's Republic of China
| | - Davide Fornacca
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, People's Republic of China.
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, People's Republic of China.
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, 671003, Yunnan, People's Republic of China.
- The Key Laboratory of Yunnan Education Department on Er'hai Catchment Conservation and Sustainable Development, Dali, 671003, Yunnan, People's Republic of China.
| | - Xiao-Yan Yang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, People's Republic of China.
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, People's Republic of China.
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, 671003, Yunnan, People's Republic of China.
- The Key Laboratory of Yunnan Education Department on Er'hai Catchment Conservation and Sustainable Development, Dali, 671003, Yunnan, People's Republic of China.
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, 671003, Yunnan, People's Republic of China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, 671003, Yunnan, People's Republic of China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region, Dali University, Dali, 671003, Yunnan, People's Republic of China
- The Key Laboratory of Yunnan Education Department on Er'hai Catchment Conservation and Sustainable Development, Dali, 671003, Yunnan, People's Republic of China
- Yunling Black-and-White Snub-Nosed Monkey Observation and Research Station of Yunnan Province, Dali, 671003, Yunnan, People's Republic of China
| |
Collapse
|
92
|
Liu N, Hu H, Ma W, Deng Y, Dimitrov D, Wang Q, Shrestha N, Su X, Feng K, Liu Y, Hao B, Zhang X, Feng X, Wang Z. Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships. MICROBIAL ECOLOGY 2023; 85:1013-1027. [PMID: 35364696 DOI: 10.1007/s00248-022-01997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/11/2022] [Indexed: 05/04/2023]
Abstract
Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.
Collapse
Affiliation(s)
- Nana Liu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huifeng Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenhong Ma
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Qinggang Wang
- Department of Ecology and Ecological Engineering, College of Resources and Environmental Sciences, and Key Laboratory of Biodiversity and Organic Farming of Beijing City, China Agricultural University, Beijing, 100193, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuqing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Baihui Hao
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Xinying Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
93
|
Ren Z, Ma K, Jia X, Wang Q, Zhang C, Li X. Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area. MICROBIAL ECOLOGY 2023; 85:904-915. [PMID: 35650293 DOI: 10.1007/s00248-022-02053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 05/04/2023]
Abstract
Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.
Collapse
Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China.
- School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xuan Jia
- College of Education for the Future, Beijing Normal University, Zhuhai, 519087, China
| | - Qing Wang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
94
|
Gong X, Liu X, Li Y, Ma K, Song W, Zhou J, Tu Q. Distinct Ecological Processes Mediate Domain-Level Differentiation in Microbial Spatial Scaling. Appl Environ Microbiol 2023; 89:e0209622. [PMID: 36815790 PMCID: PMC10056974 DOI: 10.1128/aem.02096-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
The spatial scaling of biodiversity, such as the taxa-area relationship (TAR) and distance-decay relationship (DDR), is a typical ecological pattern that is followed by both microbes and macrobes in natural ecosystems. Previous studies focusing on microbes mainly aimed to address whether and how different types of microbial taxa differ in spatial scaling patterns, leaving the underlying mechanisms largely untouched. In this study, the spatial scaling of different microbial domains and their associated ecological processes in an intertidal zone were comparatively investigated. The significant spatial scaling of biodiversity could be observed across all microbial domains, including archaea, bacteria, fungi, and protists. Among them, archaea and fungi were found with much stronger DDR slopes than those observed in bacteria and protists. For both TAR and DDR, rare subcommunities were mainly responsible for the observed spatial scaling patterns, except for the DDR of protists and bacteria. This was also evidenced by extending the TAR and DDR diversity metrics to Hill numbers. Further statistical analyses demonstrated that different microbial domains were influenced by different environmental factors and harbored distinct local community assembly processes. Of these, drift was mainly responsible for the compositional variations of bacteria and protists. Archaea were shaped by strong homogeneous selection, whereas fungi were more affected by dispersal limitation. Such differing ecological processes resulted in the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling and provides novel mechanistic insights into the diversity patterns of microbes that belong to different trophic levels. IMPORTANCE As the most diverse and numerous life form on Earth, microorganisms play indispensable roles in natural ecological processes. Revealing their diversity patterns across space and through time is of essential importance to better understand the underlying ecological mechanisms controlling the distribution and assembly of microbial communities. However, the diversity patterns and their underlying ecological mechanisms for different microbial domains and/or trophic levels require further exploration. In this study, the spatial scaling of different microbial domains and their associated ecological processes in a mudflat intertidal zone were investigated. The results showed different spatial scaling patterns for different microbial domains. Different ecological processes underlie the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling to provide novel mechanistic insights into the diversity patterns of microorganisms that belong to different trophic levels.
Collapse
Affiliation(s)
- Xiaofan Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Kai Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
| |
Collapse
|
95
|
Feng M, Du Y, Li X, Li F, Qiao J, Chen G, Huang Y. Insight into universality and characteristics of nitrate reduction coupled with arsenic oxidation in different paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161342. [PMID: 36603609 DOI: 10.1016/j.scitotenv.2022.161342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/02/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Nitrate reduction coupled with arsenic (As) oxidation strongly influences the bioavailability and toxicity of As in anaerobic environments. In the present study, five representative paddy soils developed from different parent materials were used to investigate the universality and characteristics of nitrate reduction coupled with As oxidation in paddy soils. Experimental results indicated that 99.8 % of highly toxic aqueous As(III) was transformed to dissolved As(V) and Fe-bound As(V) in the presence of nitrate within 2-8 d, suggesting that As was apt to be reserved in its low-toxic and nonlabile form after nitrate treatment. Furthermore, nitrate additions also significantly induced the higher abundance of 16S rRNA and As(III) oxidase (aioA) genes in the five paddy soils, especially in the soils developed from purple sand-earth rock and quaternary red clay, which increased by 10 and 3-5 times, respectively, after nitrate was added. Moreover, a variety of putative novel nitrate-dependent As(III)-oxidizing bacteria were identified based on metagenomic analysis, mainly including Aromatoleum, Paenibacillus, Microvirga, Herbaspirillum, Bradyrhizobium, Azospirillum. Overall, all these findings indicate that nitrate reduction coupled with As(III) oxidation is an important nitrogen-As coupling process prevalent in paddy environments and emphasize the significance of developing and popularizing nitrate-based biotechnology to control As pollution in paddy soils and reduce the risk of As compromising food security.
Collapse
Affiliation(s)
- Mi Feng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Yanhong Du
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Jiangtao Qiao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Gongning Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Yingmei Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
96
|
Wang X, Yin Y, Yu Z, Shen G, Cheng H, Tao S. Distinct distribution patterns of the abundant and rare bacteria in high plateau hot spring sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160832. [PMID: 36521602 DOI: 10.1016/j.scitotenv.2022.160832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The diversity and distribution patterns of the abundant and rare microbial sub-communities in hot spring ecosystems and their assembly mechanisms are poorly understood. The present study investigated the diversity and distribution patterns of the total, abundant, conditionally rare, and always rare taxa in the low- and moderate-temperature hot spring sediments on the Tibetan Plateau based on high-throughput 16S rRNA gene sequencing, and explored their major environmental drivers. The diversity of these four bacterial taxa showed no significant change between the low-temperature and moderate-temperature hot spring sediments, whereas the bacterial compositions were obviously different. Stochasticity dominated the bacterial sub-community assemblages, while heterogeneous selection also played an important role in shaping the abundant and conditionally rare taxa between the low-temperature and moderate-temperature hot spring sediments. No significant difference in the topological properties of co-occurrence networks was found between the conditionally rare and abundant taxa, and the connections between the paired operational taxonomic units (OTUs) were almost positive. The diversity of the total, abundant, and conditionally rare taxa was governed by the salinity of hot spring sediments, while that of the always rare taxa was determined by the content of S element. In contrast, temperature had significant direct effect on the composition of the total, abundant, and conditionally rare taxa, but relatively weak influence on that of the always rare taxa. Besides, salinity was another major environmental factor driving the composition of the abundant and rare sub-communities in the hot spring sediments. These results reveal the assembly processes and major environmental drivers that shaped different bacterial sub-communities in the hot spring sediments on the Tibetan Plateau, and indicate the importance of conditionally rare taxa in constructing bacterial communities. These findings enhance the current understanding of the ecological mechanisms maintaining the ecosystem stability and services in extreme environment.
Collapse
Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
97
|
Jin N, Yang K, Li J, Song Y, Ding A, Sun Y, Li G, Zhang D. Toxicity Characterization of Environment-Related Pollutants Using a Biospectroscopy-Bioreporter-Coupling Approach: Potential for Real-World Toxicity Determination and Source Apportionment of Multiple Pollutants. Anal Chem 2023; 95:4291-4300. [PMID: 36780247 DOI: 10.1021/acs.analchem.2c03908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Exposure to environmental pollutants occurs ubiquitously and poses many risks to human health and the ecosystem. Although many analytical methods have been developed to assess such jeopardies, the circumstances applying these means are restricted to linking the toxicities to compositions in the pollutant mixtures. The present study proposes a novel analytical approach, namely, biospectroscopy-bioreporter-coupling (BBC), to quantify and apportion the toxicities of metal ions and organic pollutants. Using a toxicity bioreporter ADPWH_recA and Raman spectroscopy, both bioluminescent signals and spectral alterations had similar dosage- and time-response behavior to the toxic compounds, validating the possibility of coupling these two methods from practical aspects. Raman spectral alterations successfully distinguished the biomarkers for different toxicity mechanisms of individual pollutants, such as ring breathing mode of DNA/RNA bases (1373 cm-1) by Cr, reactive oxygen species-induced peaks of proteins (1243 cm-1), collagen (813 cm-1), and lipids (1255 cm-1) by most metal ions, and indicative fingerprints of organic toxins. The support vector machine model had a satisfactory performance in distinguishing and apportioning toxicities of individual toxins from all input data, achieving a sensitivity of 88.54% and a specificity of 97.80%. This work set a preliminary database for Raman spectral alterations of whole-cell bioreporter response to multiple pollutants. It proved the state-of-the-art concept that the BBC approach is feasible to rapidly quantify and precisely apportion toxicities of numerous pollutant mixtures.
Collapse
Affiliation(s)
- Naifu Jin
- College of Water Sciences, Beijing Normal University, Beijing 100875, P. R. China
| | - Kai Yang
- College of Water Sciences, Beijing Normal University, Beijing 100875, P. R. China
| | - Junyi Li
- Yiqing (Suzhou) Environmental Technology Company Limited, Suzhou 215163, P. R. China
| | - Yizhi Song
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, P. R. China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing 100875, P. R. China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, P. R. China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment (Jilin University), Ministry of Education, Changchun 130021, P. R. China.,College of New Energy and Environment, Jilin University, Changchun 130021, P. R. China
| |
Collapse
|
98
|
Holman J, Hurd M, Moses PL, Mawe GM, Zhang T, Ishaq SL, Li Y. Interplay of broccoli/broccoli sprout bioactives with gut microbiota in reducing inflammation in inflammatory bowel diseases. J Nutr Biochem 2023; 113:109238. [PMID: 36442719 PMCID: PMC9974906 DOI: 10.1016/j.jnutbio.2022.109238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/21/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Inflammatory Bowel Diseases (IBD) are chronic, reoccurring, and debilitating conditions characterized by inflammation in the gastrointestinal tract, some of which can lead to more systemic complications and can include autoimmune dysfunction, a change in the taxonomic and functional structure of microbial communities in the gut, and complicated burdens in a person's daily life. Like many diseases based in chronic inflammation, research on IBD has pointed towards a multifactorial origin involving factors of the person's lifestyle, immune system, associated microbial communities, and environmental conditions. Treatment currently exists only as palliative care, and seeks to disrupt the feedback loop of symptoms by reducing inflammation and allowing as much of a return to homeostasis as possible. Various anti-inflammatory options have been explored, and this review focuses on the use of diet as an alternative means of improving gut health. Specifically, we highlight the connection between the role of sulforaphane from cruciferous vegetables in regulating inflammation and in modifying microbial communities, and to break down the role they play in IBD.
Collapse
Affiliation(s)
- Johanna Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Peter L Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA; Finch Therapeutics, Somerville, Massachusetts, USA
| | - Gary M Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Suzanne L Ishaq
- School of Food and Agriculture, University of Maine, Orono, Maine, USA.
| | - Yanyan Li
- School of Food and Agriculture, University of Maine, Orono, Maine, USA.
| |
Collapse
|
99
|
Wisnoski NI, Lennon JT. Scaling up and down: movement ecology for microorganisms. Trends Microbiol 2023; 31:242-253. [PMID: 36280521 DOI: 10.1016/j.tim.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at higher organizational levels, such as populations and communities. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements.
Collapse
Affiliation(s)
- Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, WY 82071, USA; Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
100
|
Beaugrand G. Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea. BIOLOGY 2023; 12:biology12030339. [PMID: 36979031 PMCID: PMC10044889 DOI: 10.3390/biology12030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change.
Collapse
Affiliation(s)
- Grégory Beaugrand
- CNRS, Univ. Littoral Côte d'Opale, Univ. Lille, UMR 8187 LOG, F-62930 Wimereux, France
| |
Collapse
|